I haven't seen any evidence of the gate near the church being connected to anything, having been connected to anything, having been connected from anything else, or even being designed to be passable in any iteration. There's no warp there to anything, I'm not aware of a warp leading there from anything else, in fact there's not even a placeholder object or darkened plane that marks an entrance/exit.
From what I can see, it's a flavor thing. It's where we were supposed to think that we came from (based on the shape) but it's not an actual warp or destination zone.
I'll have to check out the old Tir rebirth area to see if I can find anything on the exit from there some time though. Not sure if that old one sent you to the center of Tir with a cutscene (like the G1 final) or sent you somewhere else first.
The rebirth area is an isolated map. There's no indication you're in the actual Tir map or anywhere on it when you're at the rebirth area.