You can use either bone-in or boned, it does not matter. It will, however change the cooking time.
As previously mentioned, it was thought that leaving the bone in during cooking added flavor. However, I know of no real evidence to support this and it seems, perhaps, to apply to cooking methods that spread bone flavor--like pot roasting, where all of the flavors meld.
If you buy bone-in roasts, the meat is a little cheaper as the butcher will charge you for removing the bone. Well, it's a labor charge item, you know. You can simply cook the butt until it is done enough to pull the meat from the bone and save the money.
Boned roasts may not cook as evenly as bone-in roasts. All that cutting and no wrapping or tying (as is the case for butt) changes the way it cooks. Things will be different for a tied and boneless pork loin roast. The tying and wrapping makes it cook more like a single thickness cut of meat.
Do what turns your crank, 'cause it'll work and will be good, too.