If you are all that worried about hex nuts not fitting the cups of the trainer, how about taking a set and having the very end rounded over to fit the cup. Or, it can not be that hard to have a set machined.

I do not know if you can get extra long hex nuts that fit the axle threading or not, but those could be turned down so you can keep the same flat width for the wrench. And you could round them over using a drill and a angle grinder with a sanding disk.

My 1-ups trainer even though it cams into the rear axle to close it, has adjustable cups for the width of the wheel axle.

Tom