Sounds like something went sideways in this instance. I know the load screen doesn't display saves for the wrong ToME 4 version, i.e. b42 saves won't show up on the b43 load screen (at least that was my previous experience), but I've never seen version-valid saves left out.
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The required addons are listed in the load screen's right panel (module name at the top, version number below, then "Required addons" just under that), available addons in green, missing addons in red.
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Only the addons associated with a given save are loaded, so a vanilla ToME 4 save should always load just fine even if you've got a pile of extras.
Changing a save's addons can't be done in-game, but the addons field in a save folder's desc.lua
file can easily be changed by hand. Not as convenient, but how often does a non-developer fiddle with their addons configuration?
Most of the rest of your ideas sound like bookkeeping that would only occasionally benefit addon developers. I don't know that it should be the game's job to track the entire history of addon lineup changes for every save. If you disagree, well... you could probably make an addon that would do it for you.
In summary: it sounds like you may have found a bug; a lot of your ideas describe how it already works or, bugs squashed, is supposed to work.