### 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 (!OS::get_singleton()->get_resource_dir().is_empty()) {
		
		
		resource_path = OS::get_singleton()->get_resource_dir().replace("\\", "/");
		if (!resource_path.is_empty() && resource_path[resource_path.length() - 1] == '/') {
			resource_path = resource_path.substr(0, resource_path.length() - 1); 
		}
	}
	
	if (!p_main_pack.is_empty()) {
		bool ok = _load_resource_pack(p_main_pack);
		ERR_FAIL_COND_V_MSG(!ok, ERR_CANT_OPEN, "Cannot open resource pack '" + p_main_pack + "'.");
		Error err = _load_settings_text_or_binary("res://project.godot", "res://project.binary");
		if (err == OK && !p_ignore_override) {
			
			
			_load_settings_text(p_main_pack.get_base_dir().path_join("override.cfg"));
		}
		return err;
	}
	String exec_path = OS::get_singleton()->get_executable_path();
	if (!exec_path.is_empty()) {