### 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)
Error err;
	Ref<FileAccess> f = FileAccess::open(p_path, FileAccess::READ, &err);
	if (err != OK) {
		return err;
	}
	uint8_t hdr[4];
	f->get_buffer(hdr, 4);
	ERR_FAIL_COND_V_MSG((hdr[0] != 'E' || hdr[1] != 'C' || hdr[2] != 'F' || hdr[3] != 'G'), ERR_FILE_CORRUPT, "Corrupted header in binary project.binary (not ECFG).");
	uint32_t count = f->get_32();
	for (uint32_t i = 0; i < count; i++) {
		uint32_t slen = f->get_32();
		CharString cs;
		cs.resize(slen + 1);
		cs[slen] = 0;
		f->get_buffer((uint8_t *)cs.ptr(), slen);
		String key;
		key.parse_utf8(cs.ptr());
		uint32_t vlen = f->get_32();
		Vector<uint8_t> d;
		d.resize(vlen);
		f->get_buffer(d.ptrw(), vlen);
		Variant value;
		err = decode_variant(value, d.ptr(), d.size(), nullptr, true);
		ERR_CONTINUE_MSG(err != OK, "Error decoding property: " + key + ".");
		set(key, value);
	}
	return OK;
}
Error ProjectSettings::_load_settings_text(const String &p_path) {