I’m not sure I understand your question entirely. For transliteration of Devanagari - or whichever Brahmi derived script - here’s one edition of the Rg Veda:
I don’t care much for the transliteration, but it is clear.
For Pali texts I’m used to prefixed dots for retroflexes (K.r.s.na, for example), double vowels for longs (gacchaami), and .h for visarga and .m for the anusvaara.