Hello Tom Fowler,
I agree with your thinking about no adjustments can be made to the clutch/bell housing. What I believe the manual is referring to is about the crankshaft to tranny input shaft alignment after the engine's main bearings have been worked on. Any misalignment (out of tolerance run-out) between the crankshaft center and the clutch housing's tranny pilot hole, would need to be corrected by re-shimming the engine's main bearings, if I'm reading this correctly. Hopefully we'll find out from the experts about this one.