What is the source of the water ingress? That could be a fairly important factor here.
In any event if it was discovered at the first service, Toyota should be all over it as a fitness for purpose thing - I would be asking the question in the strongest terms of how the water got in there that they discovered and why the transmission was not properly sealed from the factory considering it's a ute for one, and two we live in a temperate climate where surface water on roads is expected.
It is definitely something Toyota will want to wiggle out of, fuck em though 100% warranty and product fitness issue. But personally I've had enough of new vehicle dealers trying to escape their liability for going out and hawking crap gear with unrealistic promises.
Unlikely (depending on the volume of lube lost) that a leak from a reused crush washer would cause the shudder issue - but then I would be expecting that a trans should survive a minor amount of water ingress for a few thousand k's with no damage to critical components. This is a very poor look for the model if this is the case, but in reality we need a little more info on what happened to the thing and how the water got in and how much there was.
Comparison, I've forded stuff with my Ranger multiple times - a couple of occasions deeper than 500mm as every exit was flooded and no option as we couldn't remain where we were. No water ingress at all in any components.
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