My wife bought a 98 4Runner cheap from a dealership that got hit with a bad hail storm. It looked BAD but, they said they had a paint-less dent repair company that could fix it. I didn't believe it but they did it. Amazing.
A few years later same truck got hit with a bad hail storm and AGAIN...
You have a positive attitude and treat people fairly. $hit happens to us all and we have decisions to make. You could have cut your losses and been pi$$ed off the rest of your life without your truck, but you persevered and you are happy with your outcome. Good for you.
I don't think you should even start it let alone drive it. It's going to get more expensive real soon. Sickens me to hear of shops that are out there doing work like this.
With regard to the above with hydrolock. I saw a Jeep 6 cyl with one rod bent into a slight S shape. It didn't knock but you could see it did not come up to top dead center anymore. It wasn't obvious unless you looked for it. That was an odd one because the damage is usually much worse.
I would...
If crank journals are "perfect" and rod bearings are not damaged, it's NOT a rod knock. Assuming he checked clearance at least with plastigage. Do you know if he considered the wrist pin?
The weirdest rod knock source I EVER saw was a cracked connecting rod. The crack was above one of the rod...