Hi Edmundo,
Good on you for this.
But it does raise the very complex and essentially insoluble issue of what is the 'urtext' of a work. Just because we have a Bach autograph, it does not mean it is the 'master'. One Bach autograph MS may differ from others of the sames work, if they exist, re corrections and differences, and where we only have copies by Kirnberger and so on, are they urtext? I won't elaborate as the contents of this discussion have been going on for decades ever since the concept of Urtext became popular in the nineteen thirties. Look at editions of the WTC - they are called Urtext by Henle for example but are a pastiche of MS sources and editorial patchwork and guessing. If you are going in to a project like this, there will be a lot of controversy, or you will simply be ignored (sorry to say it). I mention this as a Bach specialist myself (though not a tenured academic).
It's impossible to diff PDF's in practice, so I don't think that is a good idea. And again, if this is a scholarly exercise, then a learned appendix and footnotes may fare better.
But also, while lilypond is great, I assure you my edition of the Bach Flute works, if I were to do it, would almost certainly look quite different to yours, in a hundred ways. The notes may be the same, but I may set it in a way that is entirely different to your way - so there is no definitive lilypond version possible either. As an aside, as mentioned in a recent post of mine, I am going to do a version of the WTC using Bach's original clefs throughout, mostly soprano clef in the right hand. If you use treble clefs instead,a modern convention, you are immediately not 'urtext'. So many problems.
This is not at all meant to be discouraging. But you may want to study the edition engraver to produce different overlays, or scholarLY from openlilylib - and so on. These type of 'meta' tools may be more what you are after than just simple file version control.
[I would assess my email here as containing at least six large cans of wiggling worms! :-)]
Andrew