Well, so what if the airlines do have to strip the paint? The point is that the paint will get stripped, so the airframe will get tested for cracks without the paint regardless of whether the airline in question decided they wanted to go with paint or without paint during commercial operations. If the airline wants to spend the money to paint, strip, paint, strip, etc., that's their business, so long as they conduct the testing without the paint.
Most airlines don't really care about this sort of thing since eddy current testing is normally performed during heavy maintenance when the airplane is pulled out of service for weeks for such minute inspections. These "heavy checks" happen after fairly lengthy intervals after which the paint on the airframe needs to be stripped and replaced anyway just because it looks awful after a while.
It's Greg Feith, actually, and he has worked as an accident investigator for the NTSB for a long time. The NTSB (which is his background) has nothing to do with the FAA and is often at loggerheads with the FAA over this or that issue. The NTSB plays an investigatory role during accidents, incidents, etc.; they have nothing to do with the ongoing regulation or inspection requirements of the airlines, which is where this paint thing would come into play. If paint seriously got in the way of performing a proper inspection, the FAA would long ago have regulated it out of existence. Since the kind of cracks we're talking about here are not going to be visible to the naked eye anyway, there's no problem with paint so long as your testing methodology is adequate to detect the metal weakness with the paint present; if it's not, the paint has to be stripped before testing.
Bottom line, paint is not an issue.