I have a 3 cup aluminum bialetti that I've had for a year. One thing that bothers me is that there are burrs around the edges on the upper section that trap coffee and are hard to clean. I have some fine needle files that could take care of it, but I don't know if there is any plating that I would be removing if I were to file it. I'm also thinking about filing down the partial thread as it's gotten pretty damaged and is a little gritty.
It’s safe as far as material is concerned: Aluminum is typically not coated, it forms its own protective layer of aluminum oxide pretty much as soon as the bare metal is exposed to oxygen and water (both available in air).
I would however be careful with everything that could affect the “grip” of the threads. Remember that the water chamber is pressurized when heated and you want to be very sure that the seal isn’t compromised.