The more stages, the less favorable your ratio fuel+propellant / dry mass. When you add stages, you add engines, tanks, systems... that you then have to haul up

The more stages, the less favorable your ratio fuel+propellant / dry mass. When you add stages, you add engines, tanks, systems... that you then have to haul up to the next stage, making your lower stages heavier. Rocket equation again. 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.