1. Kinda weird that it took this long to find since I think this has been there since the beginning. Now it's finally working correctly.
2. I think this happens when a permanent gem is added on top of a temporary one which then kinda "glues" the temporary one there too.
3. Seemed to be the case yes. Fixed now.
4. This was actually just happening on a case like in the video where your way was also blocked by a heretic. That triggered the "end check" to be ran earlier and didn't take pylon additions into account.