The main difference in the 6 volt and 12 volt starter armature is the diameter. I believe the 6V is bigger, so the 12V starter drive won't fit at all. You mention that the engine is from a 12 volt car with an automatic trans.- - - - -if you've still got the stomp start, I'll bet somebody re-used the 6 volt flywheel, starter, and bellhousing. If you've got a key start, it could have either 6 or 12 volt, as the pre-1955 powerglide cars had key start 6 volt setups.
Jerry