Yeah, so it is important to negotiate your pricing relative to MSRP or Invoice, just like you would if the car was sitting there, and get it in writing, of course you will not know the actual price, so you are negotiating for something like a percentage off MSRP or under / over invoice. Like the sales price will be $500 under invoice.
Most likely the best you are going to get is MSRP or something like $500 off MSRP, because there is obviously not enough supply to meet demand.
Negotiate there will be no add-ons like window tinting, nitrogen in the tites, or ceramic coatings or other non-manufacturer installed accessories, then yes, make a refundable deposit. It should be refundable for any reason, not just if they can't get you the car. Then get copies of the written paperwork.
I think a deposit of $500-1000 is reasonable, but it must be refundable and must be credited against the final purchase price on delivery.
The whole process sucks a little more than the normal buying process, because you have to think about everything up front and get a bunch of things in writing. At the end of the process they will have all the leverage because you have waited 12 months or longer for a car you really want, and they will know you are unlikely to walk because doing so would mean going to the back of the line and waiting for another 12+ months, and if there are those kind of waiting lists, they know they can sell the car in less than 3 phone calls so they have no risk whatsoever if you do walk.
Reach out to aggiepaintrain, hopefully he'll find this thread, he has a connection to a Toyota dealer maybe in Austin? Someone else has one too, but I am at a loss for their username at the moment. They'll at least connect you with a dealer that is honest, and even if the deal they have is slightly worse than what you find on your own, it will take some of the back-end risk out of working with a complete stranger.