To not put too fine a point on it. BMW can pick up tunes, finish and klaar. They don't even have to go look for it, their diagnostic software shows it up straight away.
It works by comparing the checksum in the ECU against a list of dealer checksums and if they different, it pops up a screen and shows which modules are affected. I've looked at quite a few cars with tunes and picked it up every time.
I'm sure there are tuners out there that's more clever about it, but I've yet to see it. Point is, if you have MP don't go for a tune. It's just not worth it