I know exactly what you mean, as this is my method. We bought the cheap vinyl peel-& stick sq. ft. tiles and lined the entire floor, including nesting box area, with them, then ran a bead of waterproofing sealer around the seams.
I use a combo of pine shavings, pine pellets & chopped straw in my deep bedding system. I don't keep water in their coop, but even when they scratch and toss the bedding around until they reach the vinyl, then poop, it scrapes right off.
It also makes cleaning easier, as I toss the bedding myself, the dried poops sift down to the vinyl, and I can scoop them out using my dustpan, then redistribute the bedding. I do this every other week in dry weather, more often if they spend more time in the coop because of rain.