### 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)
ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
#ifdef DEBUG_METHODS_ENABLED
	props[p_name].ignore_value_in_docs = p_ignore;
#endif
}
bool ProjectSettings::get_ignore_value_in_docs(const String &p_name) const {
	ERR_FAIL_COND_V_MSG(!props.has(p_name), false, "Request for nonexistent project setting: " + p_name + ".");
#ifdef DEBUG_METHODS_ENABLED
	return props[p_name].ignore_value_in_docs;
#else
	return false;
#endif
}
String ProjectSettings::globalize_path(const String &p_path) const {
	if (p_path.begins_with("res://")) {
		if (!resource_path.is_empty()) {
			return p_path.replace("res:/", resource_path);
		}
		return p_path.replace("res://", "");
	} else if (p_path.begins_with("user://")) {
		String data_dir = OS::get_singleton()->get_user_data_dir();
		if (!data_dir.is_empty()) {
			return p_path.replace("user:/", data_dir);
		}
		return p_path.replace("user://", "");
	}
	return p_path;
}
bool ProjectSettings::_set(const StringName &p_name, const Variant &p_value) {