Till, maybe I am not explaining this well enough, I will try again.
I think that an ISPConfig limit could be implemented. Right now, If I as admin set that a user can assign to site a max space limit of 500 mb, the user can't assign more than that.
What I propose to implement is this:
A user has a global limit of 500, and the user can set a max 500mb for site and 500mb for mailbox; so if the user allows 490 MBto site it will be set in linux fs, and next if the user try to create a mailbox of 20 MB, ISPConfig will stop the operation because 490+20=510 > 500 of max global limit; so, the user can't create the mailbox. The mailbox will be created only if it is set to 10 MB of space.
What I say, is that space must be manage by ispconfig before applying changes, it will not touch fs or courier/dovecot if the space assigned is more than max overall space limit.