Sandhi-conventions for critical editions

[Birgit Kellner]

I would like to have as many opinions as possible on Sandhi-conventions in
critical editions of Sanskrit texts, especially on what to do with nasals
(sounds like the title a "teach yourself"-volume: "What to do with nasals:
Ten steps to nasal perfection":)). 

The manuscript I am currently using, for example, generally (i.e. in the
overwhelming  majority of cases)
assimilates nasals in pausa, when the following word starts with ca, ta or
va  (i.e. ki~n ca, kin tu, kim vaa). It also sometimes writes ma in pausa,
when the following word begins with bha, ba or na, but never with any other
consonants. 

Is one supposed to replace ma at the end of a word, just as the scribe seems
to have done, by the homorganic nasal (although he does not follow this
policy throughout the text), is one supposed to carry out this replacement
only within compounds? In either case, why?