I think the difference between being protected and being rebooked is that when you are protected you are, in a sense, "double booked" because you don't lose your original confirmed seat until the gate agent drops your seat when it's clear you won't make it.
What's incredibly mystifying to me, though, is when you make your connection and have been reprotected, your protection doesn't automatically cancel out (at least in my experience).
The above matches my experience as well. Cheers.