Can't say it any clearer.
Raise the stack limit on materials (Spirit Bloom, Relic Iron, etc.)
If you say you can't increase the vault size, then at least make it so we don't have to waste space on 200 limit stacks of mats... Weapon Parts, for example, don't have a limit, why mats???
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Why would you collect that much of each one? Doubt they thought people would horde materials like that, seeing you use 8+ at a time. You have 3 chars, make one a murk. Plain and simple.