The data that needs to be transmitted (apart from the flight details) is contained in the passport, so it is possible that the airline might have been able to transmit the info by extracting it from your passport.
The legislation does not apply to flights originating in the Schengen area, and I do agree with you that it seems illogical. In fact, I even have my doubts as to the compatibility of the legislation with EU law, to the extent that it applies to some intra-EU flights and not others.