### 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)
vc.flags = PROPERTY_USAGE_EDITOR | PROPERTY_USAGE_STORAGE;
		}
		if (v->internal) {
			vc.flags |= PROPERTY_USAGE_INTERNAL;
		}
		if (v->basic) {
			vc.flags |= PROPERTY_USAGE_EDITOR_BASIC_SETTING;
		}
		if (v->restart_if_changed) {
			vc.flags |= PROPERTY_USAGE_RESTART_IF_CHANGED;
		}
		vclist.insert(vc);
	}
	for (const _VCSort &E : vclist) {
		String prop_info_name = E.name;
		int dot = prop_info_name.find(".");
		if (dot != -1 && !custom_prop_info.has(prop_info_name)) {
			prop_info_name = prop_info_name.substr(0, dot);
		}
		if (custom_prop_info.has(prop_info_name)) {
			PropertyInfo pi = custom_prop_info[prop_info_name];
			pi.name = E.name;
			pi.usage = E.flags;
			p_list->push_back(pi);
		} else {
			p_list->push_back(PropertyInfo(E.type, E.name, PROPERTY_HINT_NONE, "", E.flags));
		}
	}
}
bool ProjectSettings::_load_resource_pack(const String &p_pack, bool p_replace_files, int p_offset) {