Yes, in fact they do. Read the
magnusson moss act, if a dealer or motor company wants to deny a claim they have to have a reason why and they have to be able to reasonably prove that the thing they are claiming caused the failure did so.
Do you know what the tune parameters are?
Do you know for a fact that this tune actually changed anything in the transmission logic that would actually cause damage? Do you even know what the optional parameters are and which ones can cause damage?
For that matter do you know what the damage inside the transmission actually is and if its something that could have even been caused by a tune?
Do you know for a fact that the tune itself actually increased the output of the engine beyond the rated power handling capability of the transmission, changed the power enrichment or turbo behavior in such a way to create a torque curve that could be harmful to transmission parts?
Do you know if it changed the boost level at peak torque output, or increased peak torque output? Because if it didn't raise the peak torque value its awfully hard to blame the tune.
Do you know if the tune changed the shift point strategy, clutch engagement logic, line pressures or changed anything that actually could have caused damage to the transmission?
Do you know with certainty that this was a hard parts or wear item failure inside the transmission?
I would love to know what you do, maybe it would change my perspective on the issue. Unless you know any of those items you cannot outright say that the warranty can or even should be denied. For all we know there is an electronic component that simply failed and is completely unrelated to the problems the OP is facing.
Until you can actually justify why " A tune " automatically voids a power train warranty please stop the fear mongering, it hurts the enthusiast, hurts the aftermarket, and hurts the OEM. Thanks.