Instead of running staggered jetting like the srx , on the viper they run straight jetting and lowered the comp on the PTO. All about cooling. Larger jets better piston cooling, lower comp less heat. This was a poor design by Yamaha hence all the cooling issues on the vipers.
My Yamaha Waverunner runs lower compression on the PTO side, and supposedly the ignition timing is retarded too. I think the PTO side just sees a higher load, hence it needs more babying. Better cooling, bigger jets, less timing - these are all bandaids.