I believe that I know exactly why, but I've never read anything specific put out by H-D... Does anyone know of such an explanation?... I'd certainly like to read it!

 

Seems pretty straightforward? To ease assembly and remove room for error. Just look at all the failed IPB's on 2006 Dyna's that don't have dowels in the inner primary/transmission mating surface.

It certainly helped having dowels when I mated my transmission with my engine. .ensured the gasket lined up properly to prevent leaks.