You're on the right track for sure.
I've heard some strange things over the years but this one is way up there on the list of odd ones. Filling the bike vertically versus on the side stand isn't your problem.
The tank on your bike, assuming it is stock, is a single tank. It has no split in the center and has one filler neck. In the past there could be issues if a crossover tube was blocked and the fuel didn't transfer but that is not an issue with your bike.
My guess is that your problem is caused by a blocked tank vent. If it gets blocked then air will not enter the tank and, as the fuel is drawn out, a vacuum is formed and the fuel flow can stop. When the tank is full this vacuum will form much more quickly.
The simplest way to know if this is the issue is to recreate the stall and then open the fuel cap to allow air in. You may hear air being sucked in. If the bike starts back up immediately then you know you have a vent issue. The vent is a small curved tube on the top front of the tank toward the right side of the frame. There should be a rubber hose attached to it. There is also a check valve in that line back near the seat area. It can stick closed. I would check to insure this is open.
If the venting is not the problem then the fuel pump or lines are the likely issue. Some more in depth troubleshooting will need to be done to determine where the problem lies.
I hope this helps. Please let me know if I can be of further assistance. Also, please leave a positive rating for my service today. Thanks, P.J.