I can’t say anything specific about Saṃgharatna, but I’m presently wrapping up my dissertation on Vanaratna (1384-1468), who I’m sure you know was a contemporary of Lokottara and said to hail from the same generic “eastern India.” Vanaratna is even referenced in Śākya mchog ldan’s rnam thar in close proximity to passages on Lokottara. Vanaratna was from Sadnagara, which I couldn’t definitively identify, but which based on evidence from Vanaratna's rnam thar I can locate with reasonable certainty in the easternmost Bengal delta, some distance north of Chittagong, possibly up in the Tripura hills (It is clear that Vanaratna is not from Chittagong proper, as is too often reported). All this is to say that this area was still nominally an active Buddhist region at the turn of the 15th century, though it was in steep decline. Thus this is one area to look at as a possible location for Saṃgharatna. 

If you haven’t done so already, have a look at Arthur McKeown’s Guardian of a Dying Flame, a study of another, slightly earlier figure from the same region, Śāriputra (1335-1426). He speculates on the possible locations of Śāriputra's birthplace, which was also in eastern India. 

Are you familiar with Tāranātha’s description of the eastern region of “Koki,” which while not without problems is a useful description of the Tibetan understanding of Buddhism in Eastern India and SE Asia. The passage beings somewhere around folio 131v in his history of India (see BDRC no. W22276)

I was genuinely intrigued by the little I read about Lokottara in Śākya mchog ldan’s rnam thar, so I’m glad to hear work is being done on him. 

Best wishes,

Ryan

Ryan Damron
Doctoral Candidate
Department of South and Southeast Asian Studies
University of California, Berkeley
7233 Dwinelle Hall
Berkeley, CA 94720-2520
rdamron@berkeley.edu