Good point. I suppose if you really wanted to be safe, you could duplicate the factory presets in the user folder, and then rename them there. You'd basically end up with duplicates of the settings, but with different names.
I think there is definite value in NOT changing the factory presets, but rather saving them in your user folder, either with the same name, or with asterisks or whatever you choose.
This way, when you upgrade to a newer version of Logic (which WILL happen sooner or later), your personal selection will be untouched - there is always a danger of Factory folders being overwritten during an upgrade.
I keep "selection" folders for most plugins. They come up as a separate item in plugin menus and I know I can go straight there for my favourites or modified sounds. Also, these files are so small, it makes virtually no difference to your disk space.