I think part of it is what speakers are being used. The Jose sounds quite different through Greenbacks vs V30s, for example. Keep in mind that the original Joses were usually Plexis that typically sound best through Greenbacks. The Jose isn't any different, and when the mods are turned off, does a pretty good Plexi complete with plenty of kerrang.
The Jose is the most raw Friedman I've played. I've also got a BE100DLX, and while I can understand why some say it's smoother or more polished, I don't buy into that, either. It can be plenty raw, depends on how it's dialed in. I've got a Herbert, too. If I treat it as a typical amp, I can see why people think it doesn't cut, but that's also wrong. I'm not afraid to set the knobs to whatever sounds best to me and my Herbert has plenty of top end and bite. Not to compare sounds, rather techniques, but think about a Mesa Mark. If you set everything to 5, it's gonna sound rough, but once you figure out how to dial it in, watch out. All of the above have their own sound. They may or may not be for everyone, but for me, I love them all for what they are.
I like my Jose best with higher output pickups, but again, this is what most people were using when Jose designed his mods. I think it still sounds great with PAFs, too, just not my preference for this amp. I have no problem getting pinch harmonics with either, but to be fair, I can get pinch harmonics on my acoustics, too.