I understand why they wouldn't transfer the discount to a new "custom order", but they should give you another matching inventory vehicle. If I understand correctly - it seems they *would* do that, but they don't have any of the same configuration.
You don't get to see the actual inventory vehicles from the website, so it's impossible to see a misalignment like this. I truly hope they accommodate you.
I'm usually one to suggest "just live with it" to other posters that have small misalignments... but this looks really bad and will no doubt catch debris / road salt / etc that will encourage rust, paint deterioration, and other issues.
If I were in your shoes, I would just be persistent that you want a vehicle without this major misalignment that matches your specs.
It may be the case that a different vehicle won't have the same discount, but you should not lose your order fee or any other monies paid because of this.
Strongly suggest being unfathomably polite to the very end. Getting angry or losing your cool won't help in this case, and Tesla sales employees aren't paid commission... you really need a sympathetic advocate on the inside.
I have faith that this will resolve well and that you'll be happy owning the world's best selling vehicle in the near future. Good luck! And welcome to the forums!