Any issues with storing a vault inside a vault?

Theoretically, it’s possible to store a vault inside a vault. However, I wouldn’t recommend it because it has a significant impact on performance. And it also won’t work with iOS because there is no workflow for that.

Since the passwords are already different, I would just put the vaults next to each other. I understand what you’re trying to achieve (similar to two-factor) but this isn’t possible with Cryptomator. Related discussion is here (and this one might also be interesting).