I'm not sure capping the skills is quite fitting. There is a BIG xp difference between using a good CPU and a cheap junk one. But look at RL computers. A simple processor can be absurdly skilled at a task.
Now capping /autonomy/? Absolutely. That makes 100% perfect sense. That's a highly complicated thing, and simple processors just wouldn't be able to manage it. So any CPU below C grade would be incapable of supporting dual roles.
Might be fitting to also limit getting the smart traits to advanced CPUs as well.
I very much, however, think that when changing CPU, there should be a loss of skills (since there's no memory module). Because as it stands, get your hands on a top of the line CPU, put it in the bot, train up, replace the CPU with cheap crap, no downsides.