Magnets repelling can cause quite a few problems. Let's take Greg Pentultimate for example. It uses magnets to hold itself together, but the magnets repel at an exact mid turn. The way to prevent this is to make a magnetic Master Pentultimate and then bandage it into a normal Pentultimate. The problem with this however is you need a bandaged Megaminx internally to make sure the Master Pentultimate is aligned. Then you have the next problem of trying to connect the Megaminx and the Master Pentultimate together, and you put a Pyraminx Crystal in between to hold each of the layers together. You then realise that what you've done is made a Pentultimate with the best mechanism, the shells mechanism. So you throw away the magnets and you have an awesome Pentultimate.
You need to check the geometry to see if it will cause any problems. Besides, if they're only for stabilising, you shouldn't have
to use them.