It's very uncommon for the missing tooth to be at zero degrees.
With Bosch systems on 4-cylinders on a lot of makes it was at 108 degrees BTDC.
The reason is that the teeth are used for controlling spark timing and a missing tooth would make that slightly more inaccurate and a whole lot more difficult to write the software correctly.
Usually there's only 1 position the flywheel will fit, because of the pattern used for the bolts. It's unlikely that it is fitted in a wrong position.