Machine shop owners are not in the business of talking themselves out of business. Think about it, if he says not to align hone, he loses the business. If you don't align hone it and there is any problem, he had said it would be OK and you'd blame him. Safest, most profitable course for him is to tell you to machine
everything
FWIW, I agree with David. Think about it. The main caps are located by the broach in the block, not by the bolts or studs. Of course, you are asking about limp-wristed SBC iron, then anything could happen.
thnx, jack vines