Some things are impossible until they aren't.
Landing boosters is an incredible engineering feat. The rocket equation is just derived from the laws of physics, it's not something you can change with great engineering.
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.
Land-anywhere and launch-anywhere are also very attractive features for places with sparse support.
I wonder if SpaceX could build a demonstration landing pad, ferry some liquid methane and liquid oxygen to, say, Guam (which is kind of part of the US, making things a bit easier) and do a suborbital hop across the globe with the starship alone without the booster, refuel, and fly back to Florida.