Looks like a limitation in AEM, here's my response from the ticket:
"This is not a bug but an implementation limitation. SAML configuration only allows to auto create a user under /home/users, however, it does not have an option to specify a custom path for users placeholder.
OOTB there, not any suitable workaround, you can possibly implement some listener that can move created users to /home/users/community or even create a workflow that can be triggered to move users.
I'll log an enhancement for future releases."