Regardless of what you think of the dude, he's a good engineer and I'd trust his data and his assessments of appropriate tolerance. That said, he only gets the worst frames sent to him. His reasonable argument to this is that there should be QC in place to keep any bikes way out of tolerance reaching the public, so take that for what it's worth. Some manufacturers (and particular periods of their manufacturing) have some notoriety--Cervelo somewhat generally (and he legitimately reams them over having a internal published manufacturing tolerance that really isn't acceptable), also a lot of Cannondales, etc. I'm working mechanic but I haven't seen enough Canyon (especially road bikes, which tend to have owners more concerned with BB performance). Take what I say with a grain of salt since I currently work for a Giant retailer, but while I've seen other manufacturing issues, they seem to have remarkably good BB shell tolerances in my experience.
I am in general in support of him giving manufacturers a hard time about their tolerances, because they really need to sort this crap out. It's a frickin' cylinder with some bearings crammed in--they should be able to get this right. There's no reason that PF BBs should suffer more issues than threaded.
Ride what you got unless your BB is actually a problem. If you have issues that seem to stem from tolerance (rather than water/grit intrusion) then take it up with them. The downside is that it's trickier with them being direct to consumer.