No one at Clausing knows why the M6-64A Pinion is 32 tooth but to answer your question of was the pinion originally 16T, yes. I called Clausing and found unfortunately that the M6-64A is on the discontinued list but they were happy to send me its drawing and also the one for M6-64. The change was made 11/06/1946. The drawing was redrawn 02/19/1973 and if there was any explanation, it wasn't copied forward.
The 32 tooth gear allows the use of the thread dial for 11.5 tpi threads. With the 16 tooth gear, you can only cut whole number threads. The actual dial remains unchanged but the rules for using it changed. 16 tooth gear: odd numbered threads, use the same mark for each pass mark, even numbered threads, every other mark. 32 tooth gear: odd numbered threads use every other mark, even numbered threads, use any mark, and half numbered threads, use the same mark for each pass.The Atlas 10" and 12" have a lead screw that is larger in diameter (either 5/8" or 3/4") than on the 6" and 8 TPI. So 1/8" pitch. And a 16 tooth pinion of a diameter such that it meshed with the lead screw. So the threading dial from the larger lathes will not fit any of the 6" because the teeth are too wide.
The early 6" (both Atlas and Craftsman) up until 1946 had a 16 tooth threading dial gear of a diameter such that it meshed with the 1/2" dia. 16 TPI lead screw. The later 6" had a larger diameter 32T threading dial gear so that it also meshed with the 1/2"-16 lead screw.
So although the early 6" and the 10" and 12" lathes all have 16T threading gears, the gears are not interchangeable. And why they changed from a 16T to a 32T no one now at Clausing knows. But I assume that it must have had to do with wear or breakage.