It is highly unlikely that any independent shop will have the Buell transmission fixture that the manual recommends, so they would be improvising just like you would have to.
You can always press the shafts in together but one at a time, pressing each shaft in a little at a time, alternating between them. The most important part is to press on the inner race of each bearing down on the shaft, being sure to not side load the bearing assemblies.
The main shaft will enter the bearing sooner than the counter shaft, so you can get it started and then worry about the counter shaft alignment. Both ends of both shafts are precision ground to fit properly in their respective bearings, so you never want to beat on them with anything that may deform the ends.