What is the availability trade off you're referring to? I don't see a downside to migrating to more limited permissions for the user. Agilebits just has to do the work to make it happen.
I would much rather have this scenario (and give 1Password access to my full Dropbox) vs having all of my data on AgileBits servers and paying for an account for families or yearly for each individual. If 1Password went to requiring vaults to be in a specific, app-permissed folder, it would break my workflows completely.
Incidentally, these sorts of access concerns are why I use KeePass over Dropbox instead of 1Password or other password managers with a hosted component.
(Caveat: I use Keepass2Android, which ironically DOES support limiting access to the Apps folder in Dropbox.)