CFA is letting you register an unknown cat? IMO the cat has to have more to the standard then just being a natural bobtail. Does he look like the breed? If not, then don't use him.
I find it hard to believe that CFA is allowing this - they are the most strict of the cat associations. I think the Bobtailed cat is a "breed" in one of the other associations (TICA or ACFA or something). Does this cat you want to bring in and start a new breed fit the standard already in place?
What kind of cats are you breeding him to? What plan do you have to establish the breed? How many other breeders are you working with? Have they seen this male to evaluate him as one to be used in the breeding program?
If you want to bring him inside and start a program you HAVE to confine him to a stud cage - he cannot be allowed outside any more. Establishing a new breed takes a ton of money - do you have the resources to breed, show, cull, and place any kitten not meeting the standard?