The way the MegaSquirt wheel decoder works, that actually would not be as good. Having the #1 tooth at TDC would mean the missing tooth is in the 30 degrees BTDC area, which is close to the spark advance the engine will often be running. Having a real tooth shortly before the spark advance insures maximum accuracy. So by putting the missing tooth right after the 30 degree tooth (and in many installations, right after TDC) puts the missing tooth in a spot where it won't diminish accuracy where you need it.
I'll admit the missing tooth location was somewhat of an accident - but it turns out to work really well.