The mailbox ratelimit will always overrule the domain ratelimit.
Regarding defaults: Yes, that’s a good idea and something I can plan to implement along with a feature to set default attributes more easily via UI. As of today most options can only be overwritten via vars.inc.local and something like a default ratelimit for new mailboxes cannot be set at all. But you can set a ratelimit for domains and have all mailboxes without rl covered.
Not sure right now, but do we have a section for ratelimits in our docs in “Models”? We should put more information there…