so a couple of things.
First yes someone is running it with a sb too, so rotation doesn't seem to matter.

Two, I think you are over thinking the wheel size and tooth size.

First, there is no way for them to know which one is the short tooth till after it passes.
So my bet is it just does a cal check.
By the way I just past number 1, where do you think I am.

Now the only concern I have is how they figure out which one is the short tooth.

Timing should not be an issue. Since they use the tooth as the trigger. My bet is that the smaller diameter of the mopar wheel will make up for the size of the teeth since the ford wheel is probably proportionally the same. But I don't want to do the math to figure it out this morning. But basically what I am saying is, why have that complex table programmed in if you don't need it. What purpose would it server to calculate timing based on the size of the teeth.

back to how they figure out the short tooth.
my concern there is as you speculated, why not have a table based on rpm for how long it takes that tooth to pass to say yep, here is number 1.

But I say that isn't fluid enough.
Wouldn't it be smarter to say, take the average of the last 7 teeth and compare to the next one.
if it is shorter call it number 1.
I understand rapid acceleration might change it, but would be easy with tps to say, you are at wot, so don't take that measurement, or take x percent difference due to accelleration.

I bet it will take the smaller wheel into account.