Sure it's possible that if you had super lightweight material for all the dry mass, 3 stages would make more sense.
You're right, there is a "real-world tradeoffs between efficiencies in the rocket equation and engineering parameters". This trade-off is unfavorable to SSTOs.
Viewed another way: if you had an SSTO, you could radically increase its payload to orbit by adding a really dumb first stage. Even a small delta-V from that stage would make the job of the "SSTO" part much easier. And SpaceX has shown that such a first stage can be straightforwardly made reusable, especially if the delta-V allows return to launch site recovery. This basically destroyed any remaining argument for SSTO.
The benefit from going from 2 to 3 stages is much less.