Bedliner is ugly. Don't hurt your jeep's appearance with it. Also, it's added weight. Sorry to bring weight up, because I'm always worrying about weight, but its true.
If you're going to spray, which I agree you should, then you should spray the entire top with black then spray clear coat. It will probably come out nicely. If it doesn't come out so nicely, then hey, it will still be better than bedliner.