Originally Posted by VidaNaPraia

No one can yet say whether Cuba will go back to the "old" system of not stamping US passports on that route. (Aduana is currently stamping all passports, which they did not previous to the relaxing of the rules by Obama.) Of course, if your passport is stamped, it is obvious to CBP on return where you have been, regardless of the route. No one can say if that would put you at risk of an eventual audit.
I have read on other travel forums that the Mexican airlines are also requiring those with US passports to fill out an affidavit, just as if they traveled direct from a US airport.