>However, these two sometimes give completely different results. For example, the Lumix LF1 has a perceptual megapixel count of 3MP, while the Sony RX1 boasts 18MP -- a 6x difference.
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>But when we compare the number of lines the camera can resolve on a resolution chart, a completely different picture emerges: The Lumix does 22, while the RX1 does only 26. This is only an 18% difference, which is worlds away from the 6x difference we calculated earlier.

Short answer: do not compare MTF50 lines per mm, compare MTF50 lines per frame height. This will give you difference similar to difference in perceptual megapixels. If you square the ratio of "lwph" between cameras you will roughly get the ratio between perceptual megapixels.

Perceptual megapixels are not bad but not too good either because characterising optical resolution with one number is oversimplistic.