I had this issue back in Godot 3.5 and hoped that it'd be gone, but Panels and some other Control Nodes still resize magically when executing another scene. This is such weird behaviour, that I have no idea where it might come from. Has anyone ever seen such a thing happen before? Here is a video of the bug in acton: https://piped.kavin.rocks/watch?v=79DYDT5qngk
My guess is it’s likely not a bug but an unexpected (by you) interaction of the tool script with whatever layout you’re doing.
If you can post example code demonstrating the problem someone will probably be able to pinpoint what’s happening.