For fasteners in the floor pans, rear baggage bulkhead, wing tips and other non-critical areas, I ran a tap thru the nutplates. They are still left with a small amount of prevailing torque, but it sure makes life easier. You should consider this, especially for fasteners that you will be installing and removing fairly often. Incidentally, if you intend on using lube on fasteners that you plan to run up to torque spec, don't. Most fastener specs are written without lube, unless a very specific type and specific amount is stated. As for stainless fasteners, I would suggest that you tap the nutplates wherever possible. As pointed out, stainless is very abrasive, and will lead to galling and thread stripping, especially on multiple re-use or with a long run-down (you can feel the heat right thru the bolt.)
Terry