I've had both. The plastic drop-in liner did far more damage than it prevented. Dirt and sand gets underneath them where it acts like sandpaper, removing paint, then moisture collects in the dirt causing rust. It did the same thing along the top of the bed rails where the liner wraps over the edge. As mentioned above, they're slick and things slide around unless tied down.
The spray-in liner was done by a shop. It was pretty thick, probably 3/16" or so, and was really durable. I didn't notice a battery had fallen over in the bed and it laid there all-day dripping acid. Cleaned it up, and the only damage was a slight discoloration of the material. It didn't eat into the liner at all. I remember the installer telling me that decades from now, that truck would probably be a rusted hulk sitting in a scrap yard with a perfect bed attached. I believe him. When I sold the truck, the bedliner was a big plus for the buyer and made for an easy sale.
I've seen quite a few DIY liners, and they just don't compare to the pro-grade ones. Thinner and less durable, they look ok as long as you never use them.