It's because you can reserve with your credit card and the OEM is responsible for the transaction fee. 10% of MSRP is like $4,000 and 1-3% of that is $40-$120. When saving 1/4 of a cent is crucial at scale, you wont be happy giving up 40-120 bucks.
I think that's the exact point of the previous comment. Don't stand for misaligned panels? Don't buy a Tesla. The free market will promote those vehicles that have a good enough value proposition over the ones that don't.
I'd rather have a misaligned panel than a garbage infotainment system since my interactions with the infotainment are significantly higher. I'm assuming you don't check 99% of the cars you see for panel issues, but if it's a Tesla, you do - it's kind of a self-fulfilling prophecy.
While Tesla can probably improve its manufacturing and QC processes over time (as they have), other OEMs have it much harder with insourcing half the vehicle components back in-house while developing great software capabilities.