Funny, the way I read that letter, especially the "particular paragraph of item #3" they reference, it sounds a lot more like they are saying "don't do this" to me. If they say "don't use M-16 bolt carriers in the assembly of AR-15 rifles", I would assume they mean as such.
They also state that they cannot "definitively tell you" that an M-16 carrier will make an AR-15 fire full auto. Well, in the standard sense, it will not. However, if the disconnector is removed from said AR-15 (ATF: "readily restorable" to full auto), the ramped M-16 bolt carrier could OCCASIONALLY allow hammer follow-through induced "doubling" of certain rounds (ATF: full auto = "more than one shot per trigger pull"). So the ATF Firearms Expert takes your AR-15 to which YOU added "M-16 parts" and he removes the disconnector (which they can justifiably do) and after several attempts gets it to fire a 2-shot "burst" with soft-primered sporting ammo. Guess what? You are now going to see them in court on an illgal M.G. charge, because the rifle "fired full auto" due to the M-16 part you added. It is not reliable automatic fire and is totally unpredictable and dangerous even, but it meets the definition of "full auto" if it happens even one time during ATF testing of that "readily restorable to full auto" rifle.
It is best to stick with notched hammers and unshrouded bolt carriers (ala SP1 pattern AR-15 parts) for this very reason. Plus, you can get the same effect with a bolt carrier weight in a semi carrier, if you feel the need.