3" nominal width in framing is common.
Correct me if I am wrong, but I do believe it is correct to interpet this requirement as 3" nominal in width, or 2 1/2". If you use a 2 x 4 flatwise, that gives you a 3 1/2" wide nailing surface. Similarly, I-joist products typically provide a nailing surface that is at least 2 1/2" wide.
Try contacting Trus Joist MacMillian.
No, APA does not currently provide an alternative to this requirement. Yes, using a different type of fastener would have some effect upon the panel's performance; however, remember that these tabulated values are based upon lab test results. Any variance from the parameters of these lab tests with the intent to obtain better design values could only be accepted if proven by another lab test. So, yes, go ahead and use wood screws, etc., but you cannot convince any plan checker that screws provide a better value than what's shown in the table for nails. (any way you look at it, you're "screwed" -- just kidding!)
Be careful in specifing the use of air guns for nail placement. Be sure that the air pressure in the gun is restricted such that the result is no more than if you used a conventional hand-held hammer. We do not want to allow the nail head to penetrate the top ply of the plywood any more than would occur with a hand-hammer.
Another thought: look into the actual size of the "10d nail" used in the nail gun -- it likely is not the same as the conventional 10d nail. However, it is often considered an acceptable substitute.
Enough said?
-Richard L. Flower, P. E.