### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Windows 10

### Issue description

The settings found in **application/config/project_settings_override** end up being written to the `res://project.godot` every time the editor is started.

I find this inconvenient, `res://project.godot` is always on the changelist in git because of this.

I think it would be better if settings with the same value as found in **application/config/project_settings_override** were persisted in `res://project.godot` **only** when set by the "editor interface" or "by code" and not by the "merge" that happens at the start of the editor.

### Steps to reproduce

1. Before opening the MRP in the editor, note **window/size/mode** value within `res://project.godot`;
2. Now open it in the editor and check the `res://project.godot`, notice that **window/size/mode** was changed by the contents of `res://project_override.cfg` (which is the **application/config/project_settings_override** file).

### Minimal reproduction project

[Projects Override Merging Into Project Godot.zip](https://github.com/godotengine/godot/files/11555239/Projects.Override.Merging.Into.Project.Godot.zip)
if (resource_path.is_empty() || (p_path.is_absolute_path() && !p_path.begins_with(resource_path))) {
		return p_path.simplify_path();
	}
	
	int p = p_path.find("://");
	bool found = false;
	if (p > 0) {
		found = true;
		for (int i = 0; i < p; i++) {
			if (!is_ascii_alphanumeric_char(p_path[i])) {
				found = false;
				break;
			}
		}
	}
	if (found) {
		return p_path.simplify_path();
	}
	Ref<DirAccess> dir = DirAccess::create(DirAccess::ACCESS_FILESYSTEM);
	String path = p_path.replace("\\", "/").simplify_path();
	if (dir->change_dir(path) == OK) {
		String cwd = dir->get_current_dir();
		cwd = cwd.replace("\\", "/");