I'll throw my 2 cents in, just based on my experience with the rephase process. I bought a junk Yamaha xs650 2 years ago for like 125 USD. Got it running and used it around town during my first year of law school. Vibration at interstate speeds was very bad: 35 min and your hands were numb, an hour and you can't feel the clutch lever anymore. no isolastics obviously but it had clip ons so I'm sure that didn't help. it was fun but started running pretty badly, lots of burning oil, and i ended up rebuilding it. somewhere along the way, i decided to make the motor a project and ended up with a pretty hopped up rephased yamaha.
first thoughts: when i got back on it and year and change later, it was so much faster than before that i only really noticed the jump in power from unrelated engine modifications. first interstate ride i remember thinking the vibrations were still pretty bad and i know i was frustrated. i did notice some difference but i remember thinking that the vibrations didnt change
Last month, i did 500 miles with two friends, one with a 70' bonneville and one with another xs650. we trade off during rides often and i have to say, there is no comparison. my bike has WAY lower vibes. that being said, it is pretty expensive to do, and if i hadn't ridden a bike with a standard crank after, i would have still been thinking mine was bad. it does help, but vibes are not gone. i see people all the time on the 650 forums claiming it eliminates vibration which is total nonsense.
I've got 8500 miles on the rephrase motor without any issues, so it seems to hold up, but time will tell