I agree with Will up to a point. Let me explain:
If you are going to install a bolt into a threaded hole, making sure the threads are clear of paint is part of that job. When you purchase a frameset or complete bicycle from Rivendell Bicycle Works, every single threaded hole THAT HAS A BOLT IN IT should have been cleared of paint with a tap. It's been my experience that every hole with a bolt in it has been clear of paint on every Rivendell frame and complete I've purchased.
If you are not going to install a bolt into a threaded hole, it is my opinion that it is preferable to leave the paint on. So, the fender eyelets down by the fork tips and rear dropouts are slightly better left painted, because generally, people don't leave bolts in those holes. As Will correctly said, it's not a big deal to clean the threads out and expose the bare metal when you are going to put a bolt in there.
Now, would it be better for Rivendell to clean all threads on all holes and install bolts in all of them, protecting the exposed metal? Yeah, maybe. I find it's pretty common practice to leave the empty ones painted over. I'll clean them out when I use them. If there is a bolt installed, then darn right the threads better have been cleaned of paint.