Sorry to seem ignorant, but can you please explain what the abbreviations MTF50 and LW/PH mean?
In the last chart/table, you compare the 60-250 at 135mm to the "70 Macro" (which company? I didn't think Pentax made one) and then there is a table listed at 100mm. Did you in fact mean the 100 WR Macro?
By your own definition, it seems that if you're going to compare a zoom to a prime, surely you need to at least make the comparison
at the same focal length (and apertures where these are common), NOT the focal length and aperture which is most advantageous to the zoom.
In the end, the issue is which primes you are exceeding. There is a difference between being better than a DA50/1.8 and being better than the DA*55/1.4, isn't there? And it's probably not hard for even a run of the mill zoom lens of today to be better than a third-rate, third-party prime of yesteryear. There has to be some sort of yardstick, otherwise you're comparing apples and oranges.
One thing I will accept from your argument, and that is that it's probably only objective indices like this which enable any sort of comparison. Also, standardisation of testing is important, and it seems to me that not all testing authorities out there agree on the metrics!!
Ultimately there is that mysterious quality called "rendering", which I'm not sure we will ever be able to quantify, any more than we can hope to quantify any aspect of human art. And that's what stops us all from ending up with the same basic lens (or set thereof) on the same basic system. Which is no help at all for LBA sufferers, but it does keep things interesting.