I can see how the two incidents are related in terms of potential disbonding issues, but firstly I'd presume that if inspection regimes have been criticised in the Air Transat incident, whereas they were not in the case of AA587, then AA had a better inspection regime and found no problems with the rudder on that aircraft.
Secondly, with AA587 you had colleagues on record as saying that Sten Molin had a tendency to hit the rudder pedals quite hard when dealing with wake encounters, and you have the AA advanced maneouvering training being criticised for teaching aggressive rudder use during loss of control situations.
Thirdly, you have the data from the number crunchers that proved that the lateral loads on the tail during the accident sequence exceeded the design limit of the vertical stabiliser, even if the rudder was new and not fatigued or repaired - in fact the stabiliser remained attached past that limit for a few seconds, so the 'patch' in fact did not degrade the strength of the structure.
As composites are used more and more in aviation, I think we are going to learn a lot more about their behaviour in flight-cycle conditions and I expect that the water-retention issue will become more clearly understood. However I doubt this will reverse the findings of the AA587 report, but I'm always ready to be wrong.