A PFC-corrected supply should ideally look mainly resistive on the AC side. If it has a high crest factor, send it back.
One could measure how much heat the boost converter generates. That might be a better way to measure small losses, rather than computing the difference between two big numbers measured with different instruments.
Or apply DC to the PFC converter input, at a few different voltages, and extrapolate the behavior for AC input. DC is a lot easier to measure than AC.