Thanks for your input on this, Roofermann. As you suggested, I did look at the Atlas warranty for the Pinnacle Pristine shingle (highlighted below) and in one part of the verbiage, it quotes code (1/8" punch through for decking below 3/4" thickness) and then later states the minimum nail length should be 1 1/4". This is a single layer reroof, same as a new application, so I have to assume the 1 1/4" length would apply. The warranty is important, and the installer is Atlas certified, so the extra length in the attic will have to be put up with.
From Atlas Warranty:
8.) FASTENING Placement of nails is critical to overall performance. High nail placement can result in separation of components and will cause delamination of the shingles after application. All nails must be driven straight with the heads flush to the shingle surface, never cutting into the shingle. Nails must not be exposed (visible) on the finished roof. Delamination after installation does not justify a warranty claim. FASTENERS: Nails must be 11 OR 12 gauge corrosion-resistant roofing nails with 3/8" minimum head. Nails must be long enough to penetrate the roof deck 3/4" or if the deck is less than 3/4" thick, the nails should be long enough to penetrate fully and extend at least 1/8" through the roof deck. Nails may be placed in the sealant line. NEW ROOFING APPLICATION (first shingle layer): 4 nails are required per shingle. The nails are to be located 7" up from the bottom edge of the shingle, with one nail placed approximately 1" from each side of the shingle, and the remaining two equally spaced between the two outer nails as illustrated in the diagram. NAILS MUST BE MINIMUM OF 1-1/4" LONG.