Pinion and carrier bearings, shims and so forth are all the same between the two Ford 8.8 designs (31 vs. 28 spline).
The difference occurs when you get out to the ends of the tube. The axle tubes are larger for the 31 spline as are the axles so the axle bearings and seals are different.
As long as your kit focuses on the differential and not the axle end, they are all the same. Not saying quality is all the same, lol. Get like Timken bearings vs. no name brand and of course you're getting a better kit.