Right, so just finished my testing. 85% of the stuff if fixed, everything involving events and dialog and whatnot works correctly, but there is still an edge case where you can still do switching, and unfortunately, its the warp tiles. So, warping is disabled if you are standing next to one of them, and there is a pretty good system to block you from swapping if you are in motion(more on that at the end), but if you start to switch, THEN move, you can still get to the warp tile from up to 3 tiles away, before the switch is done, and boom; soft-lock. To fix this by simply disabling swapping in certain spots, you would need to create a 3 tile exclusion zone around every warp tile. Given how hesitant you were to create a 1 tile "dead zone" without explanation, im not sure how much you will like the idea of 3 tiles.
Is it possible to disable movement after the switch has begun? Like maybe start an empty dialog window, or something? If you could stop the player moving during a switch, just take control away altogether, that would fix the issue all the rest of the way, right? Is there something like wait, or system.PAUSE in RPG maker?
The attached file is saves where I broke things, and a txt document that was just me writing what I found, as I found it. None of that is probably helpful, but hey, there it is.
https://file.io/S503aJme6GTs
PS: Not actually a major issue, but whatever code you are using to prevent swapping while moving seems to only work about 90% of the time, and only if the player isn't fighting the system. If you get yourself running down a straight hallway and mash W, you can sometimes swap while in motion. Probably not actually an issue, but could cause an edge case where you can occasionally do the above described bug while in motion instead of stopped. Might theoretically make 4 tile swaps possible. Haven't been able to do that myself.