Oil change center scam?

It's hard to say if they cross threaded the plug trying to put it back in, it's easy to do if a person doesn't pay attention to what they are doing. I do think that if it were already cross threaded in the pan it would be difficult coming out to begin with and they should have stopped there before taking it out and come and told you what the situation is.
But to replace the oil pan the engine needs to be supported from underneath. It looks like the driver side axle needs to come out, separate the lower control arm from the steering knuckle. and then a bunch of engine and transmission supports have to come out. So, this is not just an unbolt the oil pan type job. Unfortunately, it's your word against theirs in this situation. This would be a tough job to do in the driveway, although it looks like it could be done, but you'd have to be extra careful.

And yes, if the drain plug were that loose when you went in you would have noticed oil in your driveway. So, it was either already cross threaded and they took it out that way or they cross threaded the plug, got it all messed up and then backed it out again messing up the threads.
You can call another shop and see if they would try straightening the threads out for you with a tap kit. Depending on how bad they are. That's what I would do before paying $900.00. That's a bit much.

https://www.2carpros.com/articles/how-to-change-engine-oil-and-filter

Here are the instructions for replacing the Oil Pan if you decide to do the job yourself. Just remember to have blocks under the front right wheel and rear wheels for safety. Since you will be only removing the Driver side wheel. Disconnect the battery negative as well, so there are no shorts to Ground by accident. The fourth diagram below contains steps 9 to 18 which are specific to certain components, so they will be diagrams 5 to 12. Then go back to Diagram 4 where it lists steps 9 to 18 and supports the transmission. Then remove the small cover for the Torque Converter and then finally the Oil Pan.
There is no solid gasket for the Oil Pan, a Liquid Gasket maker is used, so the last three diagrams are those steps and the sequence for the Oil Pan bolts and their torque specs. Then everything is just reverse to put it back together. The toughest part will be getting the lower ball joint and lower control arm free of each other.

Yeah, there's no way to be exactly sure what happened. Usually for example, when it comes to a warranty there will be just a small line of paint on a bolt to indicate if it has been tampered with where a warranty would be void. If you knew that blue paint was there before you brought it in, that would tell you something. But on the other hand, the blue paint or most likely is some type of clue to prevent the drain plug from leaking. $900.00 is a lot for an oil pan but it is a lot of work to replace this pan. I'd try another shop and see if you can get it done cheaper. Oil changes are very important on these newer vehicles due to most of the variable valve timing is done by oil pressure. Keeping the oil passages clear prevents a lot of issues with those systems. So, shop around, there might be a shop that can possibly repair the threads. It depends how bad they are.