I'm certain that the reason the dealer does not want to go internally into this rebuild, is due to warrenty issues. If they have another failure with the unit, then they are responsible until the warrenty for the repair is over. Car dealers work the same way. Swap the unit out, then only responsible for the R&R labor.
I totally agree with fixing it, I'm certain that the parts are not that expensive, and the rebuild is mostly labor intense. If it were mine, and out of warrenty, I would pull it apart myself, with the help of a manual. Heck, it's just a few hydro motors isn't it? The engine drives one, and the driven one drives the second to the gear sets? Not that simple, but with proper manuals, and specs available it could be repaired. I remember the fellow who's hydro failed a few years back said his failure was traced to a sinstered bronze bushing in the pump which turned back to powder. I'm sure that this one failed simply also, with only 750hours. Lots of labor, but not impossible to rebuid. Most likely when disassembled the problem will be seen.
Now I've heard that the Kubota glide shifts are extremely complicated, and about the toughest to fix and repair. I was told that Kubota dropped the glide shift from their line also. I drove one once and didn't like it. When it shifted, it would spin the tires, and that was a almost idle. Seemed that a lot of internal wear could have been occuring.