I have a cast Scat 4.25 stroke crankshaft that I installed the large diameter pilot bushing in, I assume it was the 1.848 dimension. This mated up perfectly with a Borg Warner T10 4 speed in my 63 Galaxie. I later converted to a Tremec TKO 600 and found and additional smaller hole in front of the larger hole that had the pilot bushing. I assume this would be the 1.375 diameter, the supplied pilot bearing with the TKO 600 kit fit into this hole and mated up to the TKO 600 input shaft pilot. The counter bore in the rear of this crankshaft was also quite deep which would have allowed for additional clearance if the input shaft pilot would have extended past the front of the pilot bearing. In my case it did not extend past pilot bearing but it was nice to know there was clearance if needed.
Hopefully one of the vendors that handles these crankshafts can verify if both diameter holes are present in all Scat crankshafts, mine is a sample of one. Now, all that being said I would be checking and double checking that crankshaft end play is present during every step of the installation. It seems there is an abundance of horror stories related to tearing up the thrust bearing and crankshaft when the end play is removed for one reason or the other.