transmission info needed

I would like to put a commando mainshaft in an Atlas box so I can run a Commando clutch. I discovered a big problem....the first gear splines on the commando shaft are shorter than the ones on the Atlas shaft. It means the Atlas 1st gear will not slide on fully on the Commando shaft. Any idea why this was done? It means I cannot use the Commando mainshaft in the Atlas box.

My next thought is to see if RGM still makes the adaptor to use the Commando clutch on the Atlas mainshaft.
Any thoughts?