Been reading a bit about how the OEM bedliner scratches the bed and allows rust to occur. So should I remove the OEM bedliner all together and just put down a rug or something?

 

I have an 02 ScrewCab that had the factory Duraliner in it. I removed it this past winter so I could remove my bed bolts to lift the bed off. To my suprise my bed still looked brand new under the plastic bedliner. I had a small spot on the front of each fenderwell that the bedliner had rubbed through the paint and that was it. My truck had 47K miles and 8 years age when I took it out. I left it out cause I have plans for a spray in liner. So in my experience the bedliner didn't hurt it.

I've seen bed mats rust floors out in older trucks. You have to remove the frequently and clean under them

 

It's not a matter of the drop-ins always will or never will cause damage, it's a crapshoot.

I've pulled drop-ins out of trucks that were 3 months old with severe damage and I've pulled drop-ins out of trucks that were 5 years old with very little damage.