If could be just reading pulse from the rotating ring that it is monitoring, I have changed my ECU on my race car and they welded on a flywheel ring wheel 90 teeth with 2 missing. The ECU can see 88 pulse in a row and then a gap so it thus knows the RPM, it doesn't matter where (in my case) the ring is welded on and the firing is another issue for the ECU, it just needed initially to know the RPM and when the wheel have completed a full rotation (missing teeth) - Once this reference was known the next thing was to work out TDC in relation to the ring.
In summary, it's probably just measuring the rotating speed so I wouldn't worry where it is.
Justin Smith, February 2010