I agree with this logic to some extent, although Apple does seem to be notably less efficient at customizing computers than other manufacturers. One would hope that they have sequenced production at their plants and they're not actually doing what you described. It's pretty standard for something like this that build variations due to customers (e.g. more memory) and due to product line (e.g. hard drive size, combo vs. superdrive, etc) can be performed inline on the main assembly line (the work-in-process is tagged, visibly or electronically, to designate what goes in it). There's still a cost associated with that complexity, but it shouldn't be quite as high as if it were done offline.
In any event, though, they certainly deserve to profit off that if they can. I do hope though that those high costs are mostly profit to Apple and not actual labor costs at their plants, because that would be pretty inefficient on their part.