Heat coming up through the floor is a big deal in some TJ's. My TJ runs on the hot side and the floorboards always got warm so I addressed that a number of ways.
It is perfectly OK to wrap your exhaust under the floor area behind the cats but there are a few caveats to that. One, if you live in a wet climate, then you will rust out the exhaust due to trapped water. Two, you cannot wrap in front of the cats or the cats themselves. You can wrap your factory muffler but again, it most likely will rot due to trapped water. I originally wrapped my exhaust and it was fine until I moved onto other solutions but then I live in a fairly dry desert environment.
A body lift "may" help but in my case, it did not.
You can install additional heatproofing material "inside" the tub which will have a noticeable effect. I used the product on the following link and it has worked out very well and my wife does not really complain about the heat any more:
You can see what I did with this on my build thread. I installed factory carpet over this product with no issues.
Lastly and I do not recommend this for everyone but if you have the financial means, then it is a perfectly acceptable solution. Have your entire exhaust ceramic coated. You can see how I did this on my build thread as well.
My TJ still runs on the hot side but interior and floorboard temps are much much better now.