I don't see why that's the case for Lenovo though (which I'm most familiar with - Thinkpads), since you have to order online. They could do batches of different configurations, it might add a small delay for particular configurations, but that would be ok. What they do now, mostly limiting larger RAM/storage configs to top end CPUs, seems like an upsell (though at least their storage is usually replaceable, and aftermarket offers better price/choice, though the spare small capacity device is a waste).

In Apple's case, it simply seems like an upsell. They must have enough volume to sell lower spec, large storage capacity Macbook Airs at stores, or online.