The tires put more load on the trans, which results in more heat, and potential for more shock loading.
If a rig has been in previously and denied warrenty coverage due to abuse it will be difficult to push anything else through.
If a trans is caked in mud, it retains more heat, and can be subject to skepticism in regards to warrenty issues.
Essentially, due to the equipment on the jeep, and its prior record, they are skeptical to warrenty anything with no questions asked.
They know you wheel, and they know that with the equipment on your rig, your trans could be subject to failure.
What they are saying is, if they pull the unit and find that the problem is operator error, then they want the labor to diagnose it covered by the owner.
At least they are willing to go that far. Some will just flat out deny.