It's not clear of the 3rd owner purchased an S90 or knowingly purchased an S60 that had been "faked" to be an S90.
Tesla made a mistake, which benefited 1,2 or even all 3 owners. They then fixed the mistake.
I wonder if there are some regulations that prohibit the type of upgrade Tesla did on accident, and the $4,500 fee goes to cover the regulatory requirements necessary to upgrade a vehicle.
Otherwise, yes it's kind of bad move from a customer service point of view.
As another commenter wrote, the first blame lies with who ever rebadged the S60 as an S90 and then sold it as an S90. At somepoint one owner realized they had benefited from something without paying for it, and it's unclear if they ever tried to rectify it with Tesla.
Edit to Add Ethical Questions:
If you're at a restaurant and you get the final bill and you notice an item wasn't paid for. Do you speak up, or do you leave knowing you ate food you didn't pay for?
What if you order DoorDash, and you get extra food you didn't pay for? Do you message Doordash to charge you?
What if it's the opposite, you don't get food you did pay for? Ask DoorDash for a refund?
Finally, what if you accidentally receive a high ticket item in from an online order. 3 months later, the online retailer figures out what happened, and asks you for the item back. If you refuse to send it back, should they charge you for it?