Clutch spline alignment problems with BMW bikes goes back a long way. My 1975 R90/6 stripped its splines at ~20K miles about 20 years ago before I knew anything about the problem. I replaced everything & lubed with anti-seize paste. A year ago I checked the splines again (now maybe 45K miles) & they were OK. BUT - I also noted that when ever the engine-transmission bolts were loosened there was cyclic micro motion between the engine and the block whenever the clutch was let out. So the problem was and still is there. The lubing helped though.
The OP might want to question the rebuild quality & find out what the mechanic did to verify the alignment engine to the transmission. Threads at Pelican detail this procedure, although the threads do not check the engine's rear main bearing clearance which is also critical. If there is an alignment problem, the clutch disk is being dragged around the face of the flywheel, imposing very high loads on the engine's rear main bearing. When this rear bearing wears eggshaped, the spline once again will have to radially carry the piston forces from the engine to the transmission input bearing. In that case, even though the engine transmission alignment is correctly shifted with different pins, the rear engine main bearing should be replaced too.
Splines offer a very compact way to carry torque while allowing some axial relative motion. But if there is a radial misalignment, the spline tooth loads become very cyclic and will cause each tooth to wear as fretting corrosion. Lubing will cover the problem for a while, but the otherwise dry application in our bikes is very intolerant of misalignment.
I'd guess the engine axis and the transmission axis should radially be within maybe .003 inch TIR for good spline life. Otherwise the spline teeth don't smoothly share the torque generated load, and will soon rub out and fail.