A flash of inspiration last night showed swim this. Swim isn't sure if this is anything new or not, but thought it was worth sharing.
MDA is much more psychedelic than MDMA, and they don't actually exhibit cross-tolerance. This is quite odd, and Shulgin thought different mechanisms must exist.
The difference between MDA and MDMA is a simple N-methyl group. However, the difference between amphetamine and methamphetamine's action shows us how an N-methyl group can VASTLY increase the efficacy of a neurotransmitter uptake reverser (Methamphetamine pumps out more dopamine than amphetamine, MDMA pumps out more serotonin/dopamine than MDA.)
However, Shulgin also tells us that the N-methyl group will weaken a psychedelic drastically.
So, swim's explanation:
MDA has more psychedelic action because it is a primary amine. It has weaker dopamine/serotonin transporter reversal action due to its lack of an N-methyl group.
MDMA has less psychedelic action beacuse it's hindered by the N-methyl group. However, it acts more like a traditional amphetamine due to increased dopamine/serotonin transporter reversal action.
So both drugs have two MoAs to some degree. Is the hypothesis valid? Surely Nichols or Shulgin have done work on this.