### 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)
Variant ret = _GLOBAL_DEF(p_info.name, p_default, p_restart_if_changed, p_ignore_value_in_docs, p_basic, p_internal);
	ProjectSettings::get_singleton()->set_custom_property_info(p_info);
	return ret;
}
void ProjectSettings::_add_property_info_bind(const Dictionary &p_info) {
	ERR_FAIL_COND(!p_info.has("name"));
	ERR_FAIL_COND(!p_info.has("type"));
	PropertyInfo pinfo;
	pinfo.name = p_info["name"];
	ERR_FAIL_COND(!props.has(pinfo.name));
	pinfo.type = Variant::Type(p_info["type"].operator int());
	ERR_FAIL_INDEX(pinfo.type, Variant::VARIANT_MAX);
	if (p_info.has("hint")) {
		pinfo.hint = PropertyHint(p_info["hint"].operator int());
	}
	if (p_info.has("hint_string")) {
		pinfo.hint_string = p_info["hint_string"];
	}
	set_custom_property_info(pinfo);
}
void ProjectSettings::set_custom_property_info(const PropertyInfo &p_info) {