Todd,
Interesting observations.
I looked on the RockAuto site and found no simple way to tell the automatic starter from the stick shift. They each appeared to have ten teeth.
I wonder if there's something else going on, as in whether the depth of engagement isn't deep enough for some mysterious reason? It looks like the starter drive gear is restrained by the nose housing, so that's what appears to keep it from going too far toward the flywheel.
Here are two threads from 460Ford.com with what might be some good info:
https://www.460ford.com/forum/37-eng...ter-motor.html
and
https://www.460ford.com/forum/37-eng...ifference.html
If you really want your head to spin, do a search for "460 starter" on the 460Ford site
Maybe one of these will give you the clue you need to get it sorted out, as in "stick shift starters are shorter throw than automatics" and stuff like that!
Tom