Given whats already been said as you point out they just won't fit the components that are required for WiFI, presumably the software doesn't need a special build as it'll know from its model number whether or not to initialise and provide options for WiFI to the user.

We have our own pick and place machine at work now, and I modified our cad software to support build attributes, therefore every component on the board can be part of a specific build (and have a specific value for that build), it outputs direct to the pick and place machine. It's literally a case of "Select which options you want on this board and then upload to the machine", press start and the machine goes off placing all the components you've selected.

We try to look as far in advance as possible, what our customers are likely to want (we're talking oems here) and we build in that functionality, it's quite nice when they say "actually, could you make it do x? sure, we made provisions for that in the design". It always happens and most of the time it's a doddle to accomodate what they want.