The manual does not say anything about the two different lengths but the manual is not written for somebody without some good knowledge to start with. I have found a few other places in the manual that is wrong or not clear on directions. The part numbers are different because as you know the bolts are different. As was in my case the bolts did torque down properly but with expansion from heat one pulled up and took the threads with it. If you had your Raptor in a shop paying for the job the shop is responsible for the incorrect assembly of your motor. If it was a Yamaha shop that would be even more so. If they don't know about what they are working on and the Yamaha OEM manual does not state clearly about the bolts the dealer can take it up with Yamaha USA. It is the shops problem not yours IMO.