What can happen when you flash a bootlocked device?
Yes, with root it is typically possible to edit/remove/replace the image that is restored by the bootloader and thus prevent the ROM/recovery restoration.  Whether that is done with a custom ROM or not isn't actually relevant.  I've done something similar (editing the script that verifies/installs the recovery) on my Dell Streak with stock firmware; check out this answer.

Of course, it's always possible for the bootloader to refuse to boot the phone after you do this, though I don't know offhand of any that are that strict.