Have we ruled out simple substitution unwisely?

[asteckley]

Did our choice of transliteration alphabet influence the calculated entropy?

Much of the stuff you are suggesting would tend to increase predictability of glyph sequencing. One would expect the net result to be a lowering of the entropy even further.

I don't understand how suggesting that "aiiin" may be a variety of different combinations of letters increases predictability. It surely makes it less predictable.

Perhaps I'm not understanding your proposed application of different combinations.
In any case, you might test a few of these ideas individually—changing only one aspect of the transliteration system at a time—and then compare the entropy delta before and after each change. (That being said, I recognize that your point is not really about any of those specific suggestions, but about the consequences of overlooking how certain assumptions have become taken for granted.)