I don't know about the touch up, but I noticed this same problem in an 05 that I went and test drove the other day. I have a January build on order, and I am going to ask the MA to specify that they are to leave the drink holder OFF of my car. The MA at the time of order told me that the drink holder was standard on January and later builds, but they might be able to make a comment on the order to leave it off.
I certainly hope so. It's ugly, unfunctionable by all accounts, and now it seems as if it ruins the paint. Untypically bad design on mini's part.
The new cup holder is very easily removed -- it is held in place by the same two Torx screws that secure the downtube. Remove the two screws (T-20 on the '05), pull off the cup holder, and replace the two screws and you'd never know it was there.
The car will come from the factory with the cup holder installed but there is no reason why your MA can't remove it for you prior to delivery. It's not a January build thing, it's been coming on all the '05s so far.