I've never ridden with anything other then the stock seat so I've got nothing to compare but after the first 30,000 or so I could comfortably ride much longer 8 or 9 hours, after that I want to stop every hour or hour and a half for about fifteen minutes or so to stretch my legs (highway pegs would probably help with that) so I'm not sure if the stock seat took a long time to brake in our I just got more accustomed to riding the NC longer.
Having said that I don't remember how long I've had the sit-n-fly installed (just that it's been at least a couple years, but likely longer) and that was I big help, especially in the heat or rain.
so my specs are as follows, I'm 5'10 or 5'11 I was 230lb until just recently, after installing a handle bar riser (30mm lift) and fixing the slope on the seat made there was an immediate difference in how long I could comfortably ride, that said plenty of people have tweeked and adjusted their NC to make it fit them better and the end result is rarely exactly the same as someone else's.
It looks like you've got experience riding both time and different styles of motorcycles and you've already started diving into different threads here on the forum
Good luck with straightening out your seat situation