Well, it turns out that fully mounting the balancer onto the hub does, in fact, result in the inner portion of the hub protruding out from the front of the balancer by ~ 1/16". The crank pulley mounts around that portion onto the balancer surface. I was initially hesitant, as the hole in the crank pulley wasn't quite large enough to fit around the inner portion of the balancer hub, and that had me thinking I must have pressed too hard onto the balancer and maybe started to crush it, but no. There were simply some surface imperfections on the inner portion of the crank hub and the inner hole of the crank pulley. So I dremeled out the inner hole of the crank pulley slightly, using a sanding bit, and then followed up with emory paper to smooth it out (I also filed the outer portion of the crank hub, to try to smooth out any damage from prior hammering). Only needed to remove a very small amount and the crank pulley just slots right on there, with correct alignment to the other pulleys.
ATI manual says to use 3/8" longer bolts to mount the pulley. I initially thought that would be 1.125" but that is too long, so I went to 1" bolts and those did the job (blue loctite and 30 lb-ft).