### 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)
PackedStringArray features;
	features.append(VERSION_BRANCH);
#ifdef REAL_T_IS_DOUBLE
	features.append("Double Precision");
#endif
	return features;
}
const PackedStringArray ProjectSettings::_get_supported_features() {
	PackedStringArray features = get_required_features();
#ifdef MODULE_MONO_ENABLED
	features.append("C#");
#endif
	
	
	features.append(VERSION_BRANCH "." _MKSTR(VERSION_PATCH));
	features.append(VERSION_FULL_CONFIG);
	features.append(VERSION_FULL_BUILD);
#ifdef VULKAN_ENABLED
	features.append("Forward Plus");
	features.append("Mobile");
#endif
#ifdef GLES3_ENABLED
	features.append("GL Compatibility");
#endif
	return features;
}
const PackedStringArray ProjectSettings::get_unsupported_features(const PackedStringArray &p_project_features) {