... Well short magnums are too fat to stack vertically in a mag efficiently. but it can be done of course
http://www.armalite.com/sales/ultramag.htm
But the loss of capacity is serious.
If you are going to stack ammo horizantally in a tube mag it needs to be short and fat (and blunt), and If you are going to stack ammo vertically in a box mag it needs to be long and skinny(sharp is OK).
Also the Benelli R1 action is long enough for a long magnum rounds anyways (including .300 Rem Ultra-mag), so to chamber it for short mags you are squeezing your ammo proportions in the wrong directions unnecessarily, and sacrificing existing action length.