It's your car - do with it as you please.
I'm modifying my Mini GP as well, but as you stated - keeping all of the original parts - so if I do sell it one day the next owner can take it back to stock or use it as is. In my eyes this does nothing to devalue the car, in fact it improves the known weak areas of the car while making it more suitable for me.
As much as I can appreciate a car moth-balled in a collection, I prefer the idea of using a car.