The bearings for the differential inside of the differential carrier are for the differential. They have little or nothing to do with the axles.
The 28 spline axles are 31 spline axles turned down to 28 spline size on the ends. As far as I know, they take the same axles bearings on the banjo ends.
I think that this has been covered previously. There were no 31 spline locking differentials available until the '68 model year. Even 67 GT500's had open differentials simply because there were no locking or limited slip units available yet.
I would have to say that there is a high likeliness that Ford Engineering anticipated this because of using the thicker 31 spline axles that were machined down to take the smaller 28 spline differentials.
Even the race cars initially used the 28 spline lockers/Lokers. As with most race cars there is evidence that most serious teams would have eventually switched over to the stronger 31 spline assemblies.
The saving grace really is that the 28 splines were running behind a 289. Those can hardly be considered high torque or even high powered engines. An FE of any kind would in short order strip out the splines.
So the answer is, you should be able to swap over to 31 splines with little or no concern. I think all of the axle bearings stay the same. ;