"A bespoke maker has many limitations..." So they do. But there are bespoke makers who charge far less than some RTW makers. And there are SF members who spend just as much--no, more--time ordering and shipping back and forth shoes as I do bespeaking shoes.
Yes, good RTW trumps good bespoke on greater availability. And it often trumps in general consistency.
But with bespoke, you design the shoes. In bespoke, the shoes are made for one pair of feet--yours.
So yes, quality is only one factor. But there are factors besides quality on which bespoke trumps RTW and MTO.
You forgot to mention that there are also lousy bespoke makers. I can get a pair of bespoke from Indonesia for less than USD$200. Not sure that it will beat a pair of Loakes in overall quality, but hell yeah, it is cheaper. Cheaper because some chap in Indonesia is working at subsistence wages under hazardous conditions.
And yes, the customer "design" the shoes made for only their one pair of feet. Is this universally better for the cost and time involved?
As for design, there are good designs and there are shit designs. But with RTW you get to see the final product first. With bespoke, you are taking a punt.
As for shoes being made for one pair of feet, the normal distribution bell curve has something to say. Most RTW shoes made will fit most people, for all practical purposes, not perfectly, but good enough (look at case studies for Microsoft vs Apple, VHS vs Betamax, etc). Bespoke does not trump here at all.
Even an average or even below average RTW trumps good bespoke in availability, especially with proliferation of online. I am not sure this is even an argument at all.