That's surprising they could decline warranty for this. Is there evidence of the top being dropped? I'd think a crack like that would be an obvious reason for warranty versus the honeycomb pattern, etc. we have seen with V1.
I don't think you can go wrong either way. In my case, I'm not a fan of the wheels and tires that come with SAS (also didn't want to deal with further delays from the SAS wheel shortage). I don't dislike the look of the stock Badlands. So, I'll ride 33s until I want a change and will add a...
Do you have a walk-in order or reservation? I believe the back door link only works with reservations (ex. ########). This number would be on your DORA order sheet if your dealer provided one.
I agree with the other posts. It's easy to make a Badlands look and ride like SAS without buying the "ugly wheels and rock-throwing tires". I wouldn't personally consider resale value while buying a new vehicle. However, the stock Badlands will always be desirable.