While it's entirely possible there are mistakes, we will indeed be using transliterations of Attic pronunciations and not koine ones. Thrace has a subscript iota - look it up in any classical dictionary. Koine and modern greeks would not pronounce it, but it is pronounced as an iota in classical greek, therefore we will render it as such. By the latter part of the 2nd century BC, it seems as though the verbalization of the subscript had ceased. Classical iota subscripts are sometimes rendered in inscriptions with iotas themselves. Latin loan words like tragoedus and comoedus reflect the pronunciation also in case some additional evidence is required.