. The challenge with non-unicode fonts is that we will need to convert the unicode "mother" text to the format that each font is expecting, for each non-unicode font. This is a lot of extra work . . .these conversion programs are idiosyncratic and error prone.
That has also been my experience. If you look at the rudrayamalatantra uttarakāṇḍa in the muktabodha digital library , it was created (with the authors permission) from the file S. Malaviya used to typeset his printed edition. The file was written in a non-unicode font and I had to write a sophisticated program to convert that to a text file in Harvard-Kyoto (Kyoto-Harvard ?) transliteration. By sophisticated, I mean it was much more than just mapping from one code point to another or combining two or more code points into one or detecting if a vertical line was the bottom part of a ligature or made a preceding letter long etc. etc. . If I remember correctly, I even had to use a computer technique called "recursion" to determine preceding letters. The "debugging" (making the program correct) was a long process..
Thanks,
Harry Spier