override.cfg gets pulled into project.godot on reload when external modifications are detected

[dozingpip]

Tested versions

3.5.3.stable.mono

System information

Windows 10 - Godot 3.5.3.stable.mono

Issue description

Related to #30912 , but not quite the same.
When Godot reloads the project due to external modification, any override.cfg changes are applied directly to project.godot. External modification can happen frequently if say, I keep the project open when I do a git pull for changes from my co-developer. ( my co-dev is #30912 (comment))
His theory as to what the problem is: "There's a parameter in the project load function "p_ignore_override" which is supposed to be set to true when loading from the editor. But they forgot to set that parameter to true specifically when reloading the file due to external modifications."

Steps to reproduce

1. Open the minRepro project, and open Node2D.tscn
2. Open Node2D.tscn in a text editor
3. Modify the tscn in the text editor somehow, ie change the name of "Node2D" to "Node2Dtest" or something, and save
4. Go back to the Godot, pick "Reload" when asked
5. project.godot file has been modified to pull in the modified test window size I have in override.cfg.

Minimal reproduction project (MRP)

minRepro.zip

[KoBeWi]

I just had this happen in 4.3 beta1, but I have no idea how. It's related to reloading, but I couldn't reproduce it with the MRP and it doesn't seem to happen consistently.

There's a parameter in the project load function "p_ignore_override" which is supposed to be set to true when loading from the editor. But they forgot to set that parameter to true specifically when reloading the file due to external modifications.

That's not the case both on master and in 3.x

godot/editor/editor_node.cpp

Line 1178 in 705b7a0

ProjectSettings::get_singleton()->setup(ProjectSettings::get_singleton()->get_resource_path(), String(), true);

Unless the reload is done elsewhere.

[ace24713]

That's not the case both on master and in 3.x

Yes, it is the case on both master and in 3.x. Unless I'm mistaken p_ignore_override is the implicit 4th parameter to ProjectSettings::setup, which defaults to false on that line of code you linked. The 3rd one that's given as true there is p_upwards

see the declaration here:

godot/core/config/project_settings.h

Line 186 in 705b7a0

Error setup(const String &p_path, const String &p_main_pack, bool p_upwards = false, bool p_ignore_override = false);

[KoBeWi]

I know why I couldn't reproduce. The reload dialog buttons do the opposite of what they say.