If you mean the scores that are show in the games listings at {xf}/arcade, then, yes, IPB & v3A games will have their scores saved also.
You can also mix & match your games. That way if you have any IPB games you like you can use them along with any Mochi games that catch your attention. I personally prefer Mochi games because I know that they are allowed to be used, versus IPB & v3A games that can be found in a variety of different places, but every site admin' goes with what works best for them.