I renewed my regular tourist passport through the mail last April, (It was a non-biometric) the whole book was punched through, though when my Official Passport was renewed at FirstCall on Capitol Hill, only the cover, information page, and the back cover were punched through. The Official Passport was only valid for 2 years at a time so it was a e-passport.

The point of this, you might want wait to wait until two weeks before you travel and visit the passport agency and ask them not to punch through the visa since I'm guessing the visa is machine readable.