This will probably confuse the situation more, but I'll share anyway. I bought a new Mopar TJ 44 hsg. to replace my 35. I also bought a Super 44 kit from Superior. I had a lot of trouble getting the correct shim kit to make it work. After finally getting the backordered shim kit, it still wasn't right. The Super 44 kit uses shims outside the brg. like the Rubi setup. The difference being it is a stack of shims rather than one select fit like a Rubi uses. The rubi shims though have a smaller ID that isn't compatible with the larger brg. on the Super 44. So in the end, I ended up using a thicker master shim than what came with the "special" shim kit in order to take up the clearance between the journals in the hsg. I didn't specifically order a Rubicon 44 hsg., but the casting is appropriate, as it has the boss for the sensor used with the rubi locker, just not drilled. So basically, my experience backs what Rawbrown said regarding the hsg. being wider between the journals. The cover still isn't on. So if anyone can measure a standard 44 hsg. I can confirm this.
Now being that your going the other way, putting a rubi locker in the standard hsg. I don't know that it would be an issue. The shim kit I got for the Super44 included a master shim that was around .100" and a selection of thinner shims to add to that. So you could ptentially use that shim set(@$30 I paid, and yes the factory shim set is $300, being a former Jeep employee helped get those for free, though they didn't work)and just use the appropriate amount. The difficult part is installing a shim stack(multiple pieces) where you would normally have one select fit shim. I put the master toward the brg. and put the thinnest shims toward the hsg. to minimize the potential for distorting them when assembling. Still, it was an excersize in patience. I would confirm the hsg. dimension first.