I have always had a drop in. It does contribute to under the cover rust. One of the pros is it will protect the bottom of the bed from dings and dents. The ribs act as a support and the liner takes most of the strain. Yes things may slide around but any loose object should be secured anyways. When I am doing dirty work I tend to drop things in the bed.
I used to lease but this last one I bought out the lease. With leasing I didn't want to option up the truck just to give it back at the end. The bed liners were always thrown in for free. I had the liner out last summer and the rust is not all that bad. There is mostly scuffing of the paint. Where it rubs often it is not rusted. Just like metal stair railings that get a lot of traffic. Constant rubbing of peoples hands keeps it shiny. If I ever get the extra cash I may get it sprayed.

 

I've got a drop in. Mine hardly ever gets wet though, so rust isn't too big an issue. I have a cover on the bed and honestly the only time the liner gets wet is when I'm spraying it out.

That said, if you lift it up, there's spots where the paint is rubbed away.

I'd say spray in if your truck bed sees the elements, which is the case most of the time.

 

All I can say is that when I bought my 96 new, I considered either spray on or nothing. I'd seen the effects of a drop-in on a working truck up here in the Northwest. I got the spray-on and never regretted it. Thirteen years later I can pressure wash it, Armorall the top rails, and it looks great.

 

There's something you can always use to gauge the quality of a product. The military subcontracts to the Line-X folks, the other liner folks don't have any GOA contracts. It could be because their prices are good OR their product is the sh*t.

Anyway, I got the Line-X XTRA done. Look what they found under my plastic bed liner. Pre-owned certified my behind:

 

These came from one of the Line-X websites.

Some of the cool things they can do with spray on bed liners are Color Match and Stencils. You can't really do that with a drop in.

 

If you can afford a new 2009 truck, you can afford a good spray-in liner. I had a drop in on my previous Dakota and put LineX in my 2008 F150. The difference in looks is extreme, and I believe the protection is much better. The downside might be a higher probability of denting that shows in the bed if you slam heavy things. The LineX was sprayed over the edges in the back, behind the tailgate, which is where the Dakota was getting rather serious rusting. This should protect that area. It was also sprayed clear over the front bed lip (they obviously moved the bed to get there) and had nice crisp edges wherever the coating ended. Very nice job and clearly will fully protect the bed.

 

^^ you know about that denting....ive had some anvils and pieces of steel thrown in the back of my 01 screw, and all that happened was just some scratches. other than that its still like new.