I have replaced pots from 1 meg K to 500 k in a CIJ Jm. the difference is notable. Less trebly. Though, you have asimelar result when you roll the 1 K pot back.
But, having 500K is far easier, since most of us don't need/want the 'icepickyness" . I also lowered the value on a stock CIJ jag to 250K pots, simelar results.
(I found 250K pots far more usable then 500K in the jag, ofcourse personal preference.
Though the above is regarding talking stock japanese pu's. Imho, the pu's themselves are part of the "problem" imho. It's just they seam to act better with a lower value of pots.
As a test I also did the 500 K pot "mod" (if you prefer to call it a mod) with some AVRI pu's, simelar result, less treble, less range. Wouldn't call in an improvement.
I know some prefer to roll the pots back, recalibrate the amp (tone, treble, mid, bass, etc...) but in the end it's like a never ending search to a "thicker" tone, usually associated with the Jazzmaster. If that's your goal, go with a nice set of aftermarket pu's and keep the stock pots.
ofcourse, just my humble opinion