Firstly, are there any issues with my having done things that way? When I first did up those ligs in my PUA, I discovered that one could “complete composites” in there and it seemed that some of those slots were actually assigned to specific ligatures (which seemed a bit odd/surprising to me, since that seems antithetical to that being a “private use area”), but with my having reordered things obviously I’ve gone against those assignations.
No, that is fine. Complete Composites indeed works within the PUA, but this is not an official standard. You can read more about the reasoning here:
Introduction
The complete composites feature, which is available in FontCreator Professional, but not in the Home Edition, may be used to create common composites, or just as an aid to the design process.
Creating Composites in the Home Edition • Stacking Fractions
A composite glyph is a glyph composed of two or more glyphs. Often they are used for accented characters like é (e acute) which is a composite of e and ´ (acute accent). Fractions can be composed from superscripts and/or subscripts…
Secondly, it’s a mystery to me how this happened, but when I look at my font in FC, in my PUA I have all those alternative fractions first, followed by all my various ligatures – but if I look at my font in MainType, my PUA starts with just three of those alt fractions, followed by all my ligs, and then come all the rest of my alt fractions.
That latter isn’t a huge deal, but I have no idea how that happened! Let alone why there’s a difference between what I see in FC and what I see in MainType.
FontCreator can order glyphs by glyph index, code point, etc. MainType shows characters by code point, alternatively you can use the glyph mode to show all glyphs, sorted by glyph index.
FontCreator has a feature which allows you to reorder glyphs. It is available from the Tools menu. This will actually change the glyph index.