Very interesting and educational post, as always. I have a few things I might add, particularly relating to the 'why' as opposed to the 'how.' In other words, what are the benefits to the customer, in addition to the enhanced durability that you describe?
There are numerous benefits to a bespoke shoe. First and foremost, of course, is fit. Bespoke shoes should be made on a personalized last, preferably on lasts carved specifically for your feet -- both shape and measurements -- and styled to accommodate your desired toe shape, heel height, type of shoe, and preferred fit. For most customers, a bespoke shoe will fit better than virtually any RTW shoe, and the materials and construction of the shoe also mean that the bespoke shoe will mold to your feet better than a RTW shoe.
Next, there is the unlimited range of styles and designs that a bespoke maker can provide. In addition to the typical decisions, such as shoe type (i.e. oxford vs. derby vs. loafer/slip-on), style (wholecut, plain toe, wingtip, cap toe, u/'adelaide' throat, etc) and amount and type of brogueing and edge treatment (plain vs. gimped), there are options such as matching linings, contrasting piping/collar, number of eyelets, and treatment of facings (should the front of the shoe meet when laced, or do you want a space -- and, if so, how much -- between the two sets of eyelets?). You also can choose the thickness of the sole, the width and visibility of the welt/sole on the finished shoe (not showing, just showing, full showing), the waist/sole treatment -(plain vs bevelled, with or without a fiddleback), the bottom finish (color and design of the sole staining), the spacing of the outsole stitching (8, 10, or 12 SPI), sole edge color, and even the heel shape (square vs angled/'cuban').
Of course, quality bespoke makers also offer an almost unlimited range of leather options, as well as custom finishes.
Finally, bespoke shoes are generally lighter and often more flexible than their RTW counterparts, which can offer substantial benefits in terms of reduced fatigue after a day of walking about.
For some people, some or all of these advantages make bespoke footwear a luxury worth paying for.