As far as RAF goes, B.Net accounts are a non-issue.

Sure you use your B.Net information to get to account management.
Instead of the warcraft account information.

Once you're there, you send the RAF invite from one of the accounts which is tied to the B.Net.
And the account that uses the invite, is tied to the account which sent the invite out.
Same as always before.

I personally go with one B.Net for each WoW account.
This means I lose out on the integrated account management, and have to do it the way everyone has been for the last 4+ years.
But a single authenticator can get you into game simultaneously across all of the B.Net accounts, instead of a 30 second delay between accounts on the same B.Net.