Thanks orbitmic . It appears as a single through fare BER-MEX and I have a single ticket number (which appears to be AA as it starts with 001).

Your explanation makes sense though, maybe the OTA did repackage something. Although AA itself offers a similar mixed booking on their own website (with BA or IB flights in the first legs). I have contacted the OTA and they can't make any changes to the booking, so my final chance is to contact AA to see if there is anything they can do.

Fully agree on your final point. So far I had good experiences saving a little (not much) by buying basic fare (only if it was a steal) and then adding the luggage, but in this case I would have been better off with a "normal" economy fare including luggage.