That's really not true. Most European bikes use standard bottom bracket sizes and you can easily find dozens of compatible bottom brackets. Same goes for headsets, axles, brakes, etc...
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.
this may be true for commuting bikes that are typically lower end, but absolutely not true for higher end bikes across the model line of all mfgs. In many cases they switch year over year.
I don't understand your last sentence. There is more than one standard for many bike parts/mounts, so even when they switch (from one standard to another), that doesn't mean it's not standard all of a sudden.
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.
"Standard" doesn't really help you much. To stay with thru-axles, yes, most rear thru axles are a standard size of 12mm. But they may have a M12x1, M12x1.5 or M12x2 thread. The length of the threaded part depends on the frame. The total length depends on the frame.
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.
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.