Line-X or Rhino should add to the value, just like a Snugtop or something...provided it remains in good condition. Incidentally...I have Herculiner, Rhino and LineX on my truck. The skill of the guy doing the work makes a huge difference, make sure you look at examples of their work before choosing a shop. If they screw it up, there goes your resale value.
Devaluing modifications are generally along the lines of lifts and such...things of obvious potentially dubious value.
The original TRD 1st-gen Tundra interior kit is another item which would add to resale value.
Of course since spray-in liners don't cost much to begin with, it's not gonna be something you can ask more for, just something to add to your selling power should you choose to eventually sell it.
-Sean