Is building a stroked 318 better than a stroked 340/360?

Exactly. And that's why nobody outside of competitive racing teams are doing that. It's too much time and money and effort to do that, when that same time money and effort could be applied to big picture things.
I generally get and agree with your main point, but your skating around the fact that 99% of the mopar engines are already built with great S/R/B ratios you got to go out of your way to build a poor one. Mainly being the 408 practically all of the stroker B/RB engines have better B/S/R ratios then a 408 and a lot can be built in ideal range. Even a 543 has slightly better B/S/R ratios than a 4" 6.123 small block. So it's mainly a paid choice to build it out of your mopar engine.

But in the end of the day most seem happy with that choice.