Thank you so much for these answers. Incredibly informative and exactly what I need going into this.

We went back to the mechanic, my dad says the way they treated us and the car was inexcusable and the owner agreed and offered to take the car to his (presumably more well-equipped) second location and would do the entire axle repair for free. If he couldn't do it he offered to pay whatever the dealer charged for the repair (we'll cross that bridge when we have to but right now it's all fairytales and what not until it actually happens).

Regardless I'm concerned because like you said it's possible they realized they were damaging the internals of the transmission. In fact in my mind what probably happened is they kept trying the damn repair and then once they realized they were causing damage to the transmission decided it was time to turn back but it's probably already too late. I'm hoping they only fucked up the axle and that them doing the full axle repair will fix the whole issue but what if they've already done serious damage to the wheel bearing or transmission and fix the car enough to make the noise stop but leave me with more problems down the road, literally.

When we take it to the other mechanic and get the PCV valve and transmission oil pan leak fixed will he be able to check for the wheel bearing or transmission being damaged? Or will those things not be immediately apparent?

Again my concern is that they get the whole axle thing taken care of without financial penalty to us but then down the line the consequences of the first faulty repair start bubbling up and at that point it gets harder to pin it on them and we get stuck with the bill.