I think your example of the onyx wheel issue can show how not far-fetched this can be. They are having some unforeseen trouble sourcing a 22" wheel painted onyx, but not when painted silver. Suppose this is the only item holding up delivery of the person's car. Wouldn't it be worth it to offer them wheels in silver without a change fee and order more silver wheels from the supplier? Even if this meant that you might be receiving a number of onyx wheels down the road, I'm sure you could use them as more orders are placed. Customers were already allowed to make such changes anyway for a $500 charge, so they already needed be ready to deal with such contingencies by overstocking components initially. Tesla also benefits by closing sales and getting the full purchase price of the vehicle finally paid. I'm surprised they weren't having the DSs begging people to switch some of their design choices for free just to increase the number of cars they could finish quickly.
Everything seems so fluid, it's pointless to create more work for Tesla, their Service Center and Delivery Specialists. Turns out that they got the Onyx wheel thing sorted out quite quickly and a number of members have already reported getting their Onyx wheels. Therefore, in this particular case, allowing customers to change their wheels would have caused longer delays than just waiting for the Onyx wheels to arrive.
With so many variables shifting at once, it's pointless to try to find the quickest path through this mess. When things are this fluid, the more things you can nail down, the easier it is to manage.