I agree that the Amory chest should be increase, but its becuase we know SE will add new jobs and I'd like the space to have at least one weapon on hand for each class.

The relic thing could be addressed by making it so that having the relic equipped counts then replacing the equipped weapon after the cutscene, though I suspect that technical limitations are in play for that.

I have the Anima weapon stashed in my saddlebag, mostly because I find it amoral to trash these specific weapons (you know due to having a soul in them) but they do come in handy for these sort of transitions (though I still have to get weapons for 4 other jobs)