First let me say I am Irish and have crossed the Atlantic > 100 times in the past 15 years and what you experienced seems close to correct. You bought a ticket from BOS to SNN (its your tough luck that AA decided to stop the non-stop flight but you gained some more precious miles by seeing the beautiful ORD..). When you checked in at BOS on the outbound you were issued (I'm sure) a boarding pass that ultimately ended at SNN. So the plane crosses the Atlantic and lands in Dub.. you tell the flight crew you simply need to stay on the plane for the short 20 min flight to SNN.. cannot see what the problem is...
So you officially get off the plane in SNN and clear (relatively lax) Irish immigration, depart the air-side ... and re-check in for your return flight to the USA ( this is what I have done on MR trips to London, Zurich and Frankfurt..)... by staying on the plane I believe you caused all of the unnecessary confusion for the AA crew..
Glad you made it back to the USA.
IrishBoy
PS. the shortest time I have spent on the ground in Europe is 90 mins... anything else leaves you the risk of not making it onto the plane on the way back.
PPS. are the additional benefits at the 125K level really worth spending 2 weekends in a plane on a MR.. I'd rather sip some CA cab overlooking the Napa Valley...