The balance tool does not care about existing paths. If you care about path preservation then you shouldn't use mergerfs.balance. That said... by using the exclude path option you could exclude specific drives in the pool from being targets so you could balance files to a subset of drives. It might not be too much work to add a flag to filter targets by available directory but I'm not sure it'd work too well TBH.
It'd be cool to make a tool which would try to keep data locality while also balancing across drives but it'd be a decent amount more work than what I've done so far with a limited user base.