Eg. if your through axle breaks, good luck finding a store that stocks one in the correct length with the correct thread and the correct thread length, and even if you do, you'll probably end up paying 40€ for a small piece of metal.
The big exception right now are thru-axles, yes, but the vast majority of bikes don't use thru-axles (and there's no reason a vanmoof commuter bike would need to use those), they use quick release axles, and those are completely standard.
I've had very high end bikes where all but a couple components were standard, and those that weren't will probably become standard soon, too.
Another problem is that every manufacturer has their own standard, eg. Shimano has 24mm hollowtech bottom bracket axles, whereas SRAM has 30mm axles, and they come in a million different sizes (threaded BSA, threaded italian, 68mm wide or 73mm wide, press fit external or internal).
In any case, a bike shop will rarely have the part in stock, because there are so many of them.
Sometimes it's even worse, when a manufacturer just updates their "standard" every few years, eg. the Shimano i-Spec standard for mounting shifter levers has 4 incompatible variants.