Sorry if this is a bit of a basic question, but I'm wondering what the code point should for alternate glyphs? For example, let's say I have glyph A and I also have glyph A.ss01. What should the unicode value be for A.ss01? Should it be the same as A? Should it have a code point at all?
General practice these days is to not encode alternates. Speaking as the person who originally made/advocated the decision to PUA encode alternate glyphs in the early Adobe OpenType fonts, I will take this opportunity to say: if I had it to do over again, I would leave them unencoded. The fact that Adobe encoded those glyphs in OpenType to start with left Adobe a legacy compatibility issue so they couldn't un-encode them when revising the same fonts.
The whole reason for encoding alternate glyphs was to allow access to the most common and interesting alternate glyphs, in a world where OpenType feature support was just starting. So, there were reasons. But honestly, they didn’t get heavy use.
Things may be different for different audiences, of course. If most of your users are using apps that are not feature-savvy, or have limited feature support (e.g. MS Word), you may have good reasons to PUA-encode some or all of your alternate glyphs. For example, if I were Laura Worthington and had her audience, I might have a different take.
If you care about the ability to backwards-derive Unicode from a stream of glyphs, and you have a situation like the wacky one with the standard Latin/western f-ligatures, then sure.
So, the situation is that Unicode encoded the ff, fi, fl, ffi and ffl ligatures because they exist in ancient “expert sets” and there was a legacy compatibility issue. So, some people want to give them their Unicode codepoints. But when these glyphs are happening because of ligature behaviors, in the get-Unicode-from-the-glyph-stream situation, you want them to decode back to f and i, not the codepoint for the hardcoded fi ligature. So you can possibly “help” things by having a glyph "fi" that is encoded but has no OpenType feature relationships, and the glyph “f_i” that is unencoded and is the result of f+i and a 'liga' feature.
These are mostly corner cases, but there are some, for sure.