1) Most manufacturers give MTFs that are theoretical and not measured... i.e: that's what they think the lens should behave not how it actually behaves.
2) PF lenses and the 200-500 f5.6 seem to have a bit higher sample variation than usual. It is possible that you might have gotten lucky with the 200-500 f5.6 and unlucky with the 600mm f6.3.
3) It's been my experience that the worst way to determine the sharpness of a telephoto is to shoot a controlled test
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I know, strange, but there are a number of factors that, if you take out of the shooting, can really skew your results. For example:
a) Most long telehpoto zooms I've used start to breakdown in image quality when your subject is more than 60-70 feet away, compared to similar focal length primes.
b) Plenty of lenses underperform when shot close to their MFD.
c) Plenty of telephoto zooms that output strong results in controlled scenarios struggle when used in tougher lighting situations (contre-jour, weird reflective surfaces around the subject and so on).
d) Prime lenses always seem to behave better with regards to atmospheric haze than zooms...
4) Subject matters when assesing the sharpness of a lens... you need subjects with plenty of detail like fur or feathers rather than leaves and petals.
5) Light also matters when assesing lenses... bright, contrasty light can crush details and nunace in shots.
6) Finally there is the factor of the viewer that is assesing sharpness... I've seen plenty of people claim that their lens was sharp when in fact it was ho-hum at best just because they didn't have the experience to know what to look for.
So all that leads to situations where two lenses might look like they perform the same when shot from a tripod in flat light at a subject 20 feet away but one will constantly provide sharper results when shooting a small bird at 40 feet with a gold/red background in morning light...
P.S: one of the cool reasons to have a brick and mortar store around and maintain a good relationship with them is that you can pop down and ask to check out a lens and compare it with the one you have to make sure it is roughly in spec.