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As there are more wranglers on the trails, there are more on the city streets that never see any harse driving that helps to even out the risks. In addition, wrangler parts are more prevalent, thus less expensive.
Other than Rubicons, the axles are not that expensive, and if let's say I replace the stock axles with D60s or a Ford 8.8, they are not warrantied by the company, since they are not stock.
A stock D35 axle is about $900.00, and a few hundred more for installation. A stock Eaton E-locker is probably around 25-3000.00, with a few hundred for installation.
I know a few people with Jeeps, and only those that have modified suspensions and/or drivetrains, take them off-road, and if modified, the extended warranty will not cover the modified parts.
My youngest has a Rubicon that has never seen anything worse than his unpaved road. He washes it more than I used to wash my '03 Vette. But it is his fun car, and in the summer, the top is always off.
However, to let you know, I checked on an extended 5/100K warranty on my Jeep and it was in the 1600.00 range. I decided against it and replaced the rear end with a beefier axle.
The one strange thing about insurance is that for car insurance, my 2003 Vette was $50.00 less per year than the 2003 Jeep. Figure that one out?
The other thing that has to be taken into account is the history of the vehicle. Wranglers have a very long history, while the H3 has a very short service history.

New information.
Just went to get comparative bids on powertrain warranties between a Rubicon and a H3, and the company I had received H3 quote on appears to have gone out of business....1 source auto warranties. Surprised me, this company was one of the oldest in the business.