That's correct and is one of the reasons I thought it was done by the shop you took it to.
I don't understand the need for a new tranny when all that has to be done is split the cases, (clutch and transmission) remove the broken threaded portion of the bolt from the case, flush, inspect it for damage, reassemble and service. This repair by replacement by Hyundai is ridiculous and expensive if they aren't going to do a warranty repair.
Transmission is not that expensive;
You can do this two ways;
1. Lawyer up and take it to a regular civil lawsuit.
2. Get legal assistance and take it to small claims court for a maximum of $5K
It's pretty obvious the shop that was going doing the tranny oil change, broke the bolt with an impact gun or similar power tool. You still need to verify if the threaded portion was left in the threaded case. If it is, then you have even more evidence to present to the shop and in court. Ask the dealership that took it in to allow you to examine as I the bolt hole as I suggested or have them do it for you. Take plenty of photos when you do. Keep in mind the last time the car was at the dealership for service and multi-point inspection. They generally have it on file in the computer and can print out the actual service and inspection sheet. You'll need it, especially to confront the owner of the shop you took it too and for court.
Let the shop owner know your intention up front. Present any evidence you can acquire as above. Don't provide it to them directly but negotiate a settlement from them. This will be better for you in the long run. Stay calm, the law and evidence is on your side. Stand your ground and explain to the owner what is going to cost you out of pocket due to their direct negligence. They need to make it right no matter. This includes; alternate transportation cost for rental, out of pocket expenses for the actual repair and any direct related costs. You can explain to them it is not going to be covered under warranty by Hyundai because of their negligence and give them the option of doing the repairs out of pocket or Hyundai doing the repairs that will cost them considerably more after being presented a lawsuit n a civil court of law.
An attorney held in retainer can negotiate this for you quite well, so it's something to consider for the long haul. Don't discuss this any longer publically, is the first thing you'll be told by a lawyer. So don't talk about it until it here anymore until it's over and done with.
I hate to see anyone have to go thru this type of action but there are disreputable shops and mechanics that need to be held accountable. The mechanic who worked on the your VN isn't going to offer up anything, he's to worries about losing his job. This is the way of it, if he was going to he would have come clean at the beginning. All your conversation from this point onward needs to be with the owner of the business. No one else and keep records of your discussions. However, you might want to consult and attorney before contacting the shop owner directly.
My best wishes in a favorable result for you, to make you whole again. If you want to discuss this any further, drop me a PM.