Good question, it's your putter, your free to do what you want to it, however I don't think they'll accept it at the SC Custom Shop if you do customise it so please bear that in mind if you do want to consider repair, refurbishment or customisation in the future.

If you're looking to get a special headcover to match your new paintfill, a word of warning, there's a lot of fakes out there so check out the seller for authenticity!