Nutplates are not normally used for joints that require the full bolt strength. They do not perform as well as a regular nut whose threads come up to the material. An easy way to tell is if the bolt isn't torqued to spec, as is the case with all phillips head screws holding panels and such. These are what the OP was having trouble with, if I understood well.
It's not the locking of the nutplate that keeps the bolt from turning, that's normally only a small part of the total friction. The locking action can slow down nuisance unscrewing if the assembly wants to vibrate loose, and only after the nominal clamping friction has been defeated. A better way to accomplish the same is with loctite, for instance on the spinner and other highly cycled places.
Lubrication doesn't help if there is physical interference between the misaligned hole and the bolt. A thou of misalignment is practically impossible to see, but will greatly increase friction and cause galling and stripping. Running a tap takes care of this and doesn't damage the nutplate.
It is safe to run a tap through almost all nutplates.