Sunlight is what kills POR.HOPEFULLY,the bottom of your car will never see sunlight.But having said that,painting right before it is dry(when it's still a bit tacky) is a good idea).
Bed liner:My interior floor is going to be sprayed(as soon as the guy gets his nutso quote lower)Underneath,there are too many little noks & crannies that bedliner will NOT reach into.But POR sprayed or stuffed with a brush will.If rust gets going under bedliner,you will not know it untill it's too late.In the unlikely event that it(rust) gets under the POR,you will still be able to see it and correct it.