Custom GDExtensiom MainLoop does not work if .godot is already generated

[FireCatMagic]

Tested versions

4.4-dev3

System information

Godot v4.4.dev3 - Windows 10.0.19045 - Single-window, 1 monitor - OpenGL 3 (Compatibility) - NVIDIA GeForce RTX 4050 Laptop GPU (NVIDIA; 32.0.15.6070) - 13th Gen Intel(R) Core(TM) i5-13500HX (20 threads)

Issue description

After the .godot folder is already generated, exiting the editor and entering it again and then running the game does not allow the MainLoop to be detected

Steps to reproduce

1. Ensure .godot is not generated
2. Run the project, it works fine
   
3. Exit the editor and reopen
4. Notice no errors about GDExtension are printed in console
5. Run the game
   
6. Notice the error

Minimal reproduction project (MRP)

New Compressed (zipped) Folder.zip

[FireCatMagic]

Actually it might not be just MainLoop.

This class in my game doesn't work yet raises no errors for the GDExtension not working.

[FireCatMagic]

Actually maybe this is related to #97900