Protecting the paint does also protect it from rust. LineX may have a very slight dent protection, but certainly not much. I know they say that in their literature, but...
A "liner liner" is a piece of thin foam that goes under the drop in liner. You can buy them cut for the purpose, though to me it just looks like 1/8" ethyl foam. The first truck I bought new I had a drop in liner and when I removed it, discovered what everyone does - the paint is ruined, rubbed off in a lot of places. My next one I used a liner liner and after 5 years or so it looked like new. I have used them since. On my last one (bought new in 1999) I pulled the drop in liner in 2014 to put in LineX and the paint looked show room new except for two tiny (dime sized) places where the liner liner had rubbed through. There had been the camper in there, big (4000 lbs) machine tools, all kinds of things - certainly not unused.
Sitting here in the dealer waiting for delivery of the new truck, still thinking about this....