I think as with lot of things with learning Japanese there are going to be trade-offs either way, especially when talking about the order of learning things. For example, if someone is intent on doing individual kanji study prior to learning any word that contains a given kanji then they’re going to need to frontload some stuff which maybe could be left to later. Or, conversely, someone wants to learn the spoken language as quick as possible and focuses on learning vocab and always uses furigana, then they will have to struggle with learning to read later on. There isn’t really a “right” answer here as it depends on goals and preferences.
I think it might be useful to consider that there are “rarer kanji forms” when a word would also commonly appear in books etc without furigana (i.e., a literate person would be able to read the word without furigana assistance). This is different to truly rare kanji forms, where they would appear with furigana as even literate natives may struggle to read them. So something like 何故 is not really “rare” and will not normally appear with furigana (unless it is meant to be read as なにゆえ, which is less common), even if it is less common that なぜ, but something like 樫 (かし) would commonly be written with furigana in even books aimed at literate adults.
Essentially, there are gradations even in what “rarity” means. How to then handle learning things is then up for debate. My personal experience is that if you keep learning and reading then you’ll end up knowing what is actually common or not intuitively and if something isn’t important enough for it to stick then it is okay to forget about it anyway.
