Boring 2x12 for pipe

I have roof joists which are comprised of a lower double header (dormer common rafter) that is (2) 2x6's nail-plated together to form a 2x12. The valley rafters and dormer ridges are 2x6's. Lower double headers are 16 o.c.
IRC says that a 2x6 can have up to a 1.5" hole bored, but 2x12 can get a 3.5" hole. What I'm wondering is do I consider these 2x6's based on the [lack of] structural support offered by the nail plates, or are they consider 2x12s?
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