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
I am not changing any of the window size parameters. They are all set in the project settings and I leave them alone. When I scale the window in runtime, everything scales exactly as I want it, so that's not a problem. Nowhere in my code do I set or change the size of any control node.
My main problem is the thing I pointed out in the video. In the "level_base" scene, the blue texture at the bottom keeps scaling up when running a totally different scene. The only thing I could see making these changes in the base_level scene, would be the base_level.gd script which is a tool script. But even that only puts textures in places and does not touch the scale or size of anything. Do you think this is an actual bug I should report, or is this just me doing something silly and that makes this problem occur?