Ganesan sent a message on the ctamil list asking me to elaborate on why I think his etymologies are fanciful. Since his questions were limited to the etymologies proposed for the words viṭaṅkar and iṭaṅkar, I will limit my response to his assertions on these words. The following excerpts from his paper discusses the word viṭaṅkar:

The god Śiva in Tamil bhakti texts of the first millennium, is extolled as either nakkar or viṭaṅkar indicating Śiva’s nudity and his virile lingam in particular. [page 4].
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The last and very important Tamil name for gharial is viṭaṅkar/iṭaṅkar. In old Tamil texts, viṭai refers to the virile male of animals - bovids, caprids, antelopes, elephants. It is a verbal noun from viṭai- 'to enlarge, to thicken, to stiffen up, to stand with pride’. In the Marutam landscape, the rich landlord enjoying prostitutes is called as viṭalai, viṭaṉ. In Tamil, viṭai- > viṭaṅku- "to be erect (as lingam), male beauty, masculinity, virility, fertile." Compare viṭai:viṭaṅku with verb pairs like (i) maṭai: maṭaṅku ‘water embankment, to block’, (ii) kiṭai: kiṭaṅku ‘animal shed, godown’, (iii) malai:malaṅku ‘to be confused’, (iv) tirai: tiraṅku ‘screen’, (v) iṇai: iṇaṅku ‘to join’, (vi) picai: picaṅku ‘to knead’ etc., Śiva is called in Tamil bhakti poems like Tevaram as viṭaṅkar, and a lingam (usually emerald) is kept near Somaskanda in viṭaṅkar temples which is worshipped with reverence as viṭaṅkar [15]. viṭaṅkar, standing for either male organ (lingam) or gharial snout, gives rise to Tamil names for gharial, viṭaṅkar (> iṭaṅkar). This word is borrowed into Sanskrit as a loan from Dravidian: viṭhaṅka ’ person of dissolute habits, voluptuary’ (Cf. viṭalai in Sangam poems). In Tamil, iṭakkar ‘indecent words; terms denoting things or actions too obscene to be uttered in good society’; iṭakkar-aṭakkal ‘ euphemism to use indirect expressions to avoid words relating to sex’, iṭakkar:iṭaṅkar ‘pot’ obviously from the protuberance on the male gharial snout, iṭaṅkar ‘narrow path’ are derivable from viṭaṅkar with the loss of word-initial v-. [page 7].

I can almost label every sentence in the above excerpts as questionable. Let us examine them one by one:

The god Śiva in Tamil bhakti texts of the first millennium, is extolled as either nakkar or viṭaṅkar indicating Śiva’s nudity and his virile lingam in particular.

1. In Ganesan's entire paper, he has not referred to the DEDR entry for viṭaṅkar and he hasn't attempted to prove or disprove why the meaning of 'beauty' found in various Dravidian languages under this entry is incorrect. Since nakkar means nude, he asserts viṭaṅkar must also indicate nudity. Here is DEDR entry 5472: 

DEDR entry 5472
    Tamil 
        viṭaṅku beauty, gallantry; 
        viṭaṅkaṉ person of beauteous form; 
        veṭippu splendour. 
    Malayalam 
        veṭippu cleanness, neatness, elegance. 
    Kannada 
        beḍaṅgu, beḍagu novelty, beauty, elegance, grace, fineness, pleasantness, showiness, ostentatiousness; 
        beḍagi a showy woman, coquette. 
    Tulu 
        beḍaṅgů, beḍagů coquetry, affectation, haughtiness; 
        beḍage a charming man; 
        biḍugu coquette. 
    Telugu 
        beḍaṅgu, beḍãgu beauty, handsomeness, fineness, prettiness, grace, elegance, strength; beautiful, elegant, large, great, strong; 
        beḍãgutanamu beauty, strength; 
        beḍãgu, beḍãgāru to be beautiful; ? 
        viṅgaḍamu beautiful.

He lists Rajeshwari Ghose's work on the Tyagaraja Cult in the references, but he doesn't refer to or disucss her conclusions on the word viṭaṅkar.  On page 35, Ghose concludes: "a) The term Viṭaṅkar was used by several writers to denote a processional image b) From the references to his sitting in the Tevaciriya mantapam, issuing orders etc., it seems likely that the reference is to an anthropomorphic figure and not an aniconic one." Nowhere does she indicate that the term Viṭaṅkar has anything to do with Siva's nudity or his virile lingam.

Furthermore, the Sanskrit usage of  the words viṭaṅka in meaning of pretty, and viḍaṅga  for clever, and corresponding Assamese word  biriṅga ʻbeautifulʼ do not show any connotation of nudity or relationship with lingam. 

Let us move to his text on page 7:

In old Tamil texts, viṭai refers to the virile male of animals - bovids, caprids, antelopes, elephants.

Tamil Lexicon thinks that the word viṭai used in the meaning of bull and other male animals may be related to vṛṣa. Ganesan hasn't discussed or discarded such connection at all. Please note that the ṣ ~ ṭ correspondence is common in Sanskrit and Tamil words. For example, viṣaya ~ viṭaiyam.

It is a verbal noun from viṭai- 'to enlarge, to thicken, to stiffen up, to stand with pride’. 

Tamil Lexicon doesn't list this as the primary meaning at all. The primary meaning of viṭu- to leave, quit, part with is found in several Dravidian languages [DEDR 5393]. The meaning of "stiff" for viṭai is not found in other Dravidian languages. If I may speculate, I think, the supplementary meaning Ganesan gives is perhaps related to *viṯ-/*viṟ- [DEDR 5439] (viṟaippu numbness, stiffness, to grow stiff as from cold, become numb, shiver as from cold;). ṯ > ṭ is not uncommon in the Dravidian languages. 

Almost throughout the paper, I kept saying to myself "Tamil is not Proto-Dravidian, Tamil is not Proto-Dravidian!". You cannot reconstruct a Dravidian root without comparative evidence from other languages, preferably based on the data found two different subgroups. This paper can be rejected purely on that basis.

 In Tamil, viṭai- > viṭaṅku- "to be erect (as lingam), male beauty, masculinity, virility, fertile." Compare viṭai:viṭaṅku with verb pairs like (i) maṭai: maṭaṅku ‘water embankment, to block’, (ii) kiṭai: kiṭaṅku ‘animal shed, godown’, (iii) malai:malaṅku ‘to be confused’, (iv) tirai: tiraṅku ‘screen’, (v) iṇai: iṇaṅku ‘to join’, (vi) picai: picaṅku ‘to knead’ etc.

Addition of the formative suffix -ku is well known in the Dravidian languages (see Krishnamurti 1997), but without establishing that viṭai has anything to do with lingam, this equation falls flat on its face.

Śiva is called in Tamil bhakti poems like Tevaram as viṭaṅkar, and a lingam (usually emerald) is kept near Somaskanda in viṭaṅkar temples which is worshipped with reverence as viṭaṅkar [15].

Here Ganesan refers to Rajeshwari Ghose's book [15], but it is clear that Ganesan hasn't read her conclusions or purposefully avoids mentioning them. She clearly states that Viṭaṅkar is likely a reference to an anthropomorphic figure and not an aniconic one. She further states that "the present-day association of the term Viṭaṅka- with the liṅga of precious stone has a close parallel in the nataraja of chindambaram, where a linga made of crystal called the Candramaulisvara occupies a similar ritual status."

viṭaṅkar, standing for either male organ (lingam) or gharial snout, gives rise to Tamil names for gharial, viṭaṅkar (> iṭaṅkar).

This is big semantic leap without any justification. viṭaṅkar cannot stand for a gharial snout. viṭaṅkar is clearly a honorific form of  viṭaṅkaṉ. The -ar suffix in the Dravidian languages is a human plural suffix (also used as honorific affix), and cannot be used for non-human gharial. Therefore, viṭaṅkar > iṭaṅkar is entirely untenable.

This word is borrowed into Sanskrit as a loan from Dravidian: viṭhaṅka ’ person of dissolute habits, voluptuary’ (Cf. viṭalai in Sangam poems).

Just an opinion and speculation. 

In Tamil, iṭakkar ‘indecent words; terms denoting things or actions too obscene to be uttered in good society’.

iṭakkar has something to do with iṭakku 'Rude, saucy, disrespectful' [DEDR 433], which, I think, is missing a Telugu cognate ṭekku. Prima facie, the words related to viṭ-a-ṅku- 'beauty' and iṭ-a-kku 'Rude' appear to be derived from entirely different, unrelated etymons, and should be treated as such until there is substantial convincing evidence. Even if they are related, it doesn't say anything about the word iṭaṅkar in the meaning of crocodile or gharial.

In summary, other than wild speculation and wishful thinking, Ganesan hasn't presented any convincing evidence to make a connection between the snout of gharial and phallic linga of Siva. I think much of Ganesan's confusion stems from the fact that nakkar 'nude person, Siva' in Tamil (nakka- < Skt. nagna 'nude'), is confusingly similar to Sanskrit nakra 'crocodile'. The word nagna 'nude, naked' clearly has cognates in other Indo-European languages (Old Persian *nagna-, Greek gymnos, Latin nudus, Lithuanian nuogas, Old Church Slavonic nagu-, Russian nagoi, Old Irish nocht, Welsh noeth "bare, naked") whereas nakra 'crocodile' appears to be limited to the languages of Indian linguistic area.

Regards,
Suresh.