They indeed have the ability to do so, though they can't refuse a seat demand by a Federal Flight Marshal (nor can they tell you if the seat demand is by a Flight Marshal) though if one has called in to a Special Assistance Coordinators (SAC) and annotated their PNR indicating a necessity for a specific seat due to medical or disability needs they are much less likely to exercise that power. (Somewhere in the maze of AA policies it states seats are not guaranteed. AA, like every other airline, has wording like "force majeure" eye. that allow them to do damn near anything, but trammel the passenger in every way possible.)