The service manual explains a few rear suspension procedures such as rear shock removal, cushion lever removal, cushion rod and swing arm removal...there doesn't seem to be a particular order of removing the bolts that applies to all of them. After having a look at my bike, it appears there's no way you'd get a socket on the lower rear shock mount without first clearing the lower end of the cushion rods. ...so I'm going to go with "NO" it doesn't really matter if any of the rear suspension bolts are wrenched upon without being supported by all of the other bolts and parts of the rear suspension. Apparently, there's no harm that will come to the bearings when the parts twist from wrenching.
Now that I think about it, I replaced the rear shock on my Kawi and I had the same question. Like the busa, it was impossible to wrench that lower shock bolt without removing the lower cushion rod bolt and clearing the cushion rods out of the way.
As it turns out, I will have to remove the whole exhaust up to the headers if I want to get a wrench on the front cushion lever nut. I'm calling it quits on the project for now. I'm just putting the bike back together as/OEM, packing it up and heading to Michigan. I'll finish this once I get settled there. I have an illustrated write up in progress and I'll post it when I'm finished.