Doug, I can't say for sure about an advantage with cutting it deeper. I just brought it up because I have never seen a pinion nut at the end of the yoke before. I have seen quite a few 9 inches, set up 8.8s, and done numerous pinion seals on anything from a 7.5-10.5" Ford and occaisional Chrysler and GMs. I haven't seen any of those that didn't have at least 2 1/2- 3 threads showing. Maybe it is just the peace of mind factor for me. Integrity wise, it should work though.
At any rate, best of luck with the new setup and have fun at DW!
I apologize to everyone if I have annoyed with my ramblings, I'll shut up now......