Never used it, but yes water could come in under the cover, unless you have a another cover on top of that. You can save some $$ too, and get a spray in one as well. Mine came with one from the factory, however other third-party companies can do it as well.
However, water under the cover is irrelevant on an aluminum bed. For that matter, it's irrelevant on a steel bed. My 2013 F-150 has a Dualliner, which is a front, side, and tailgate plastic insert (panels), and a rubber mat on the bottom. People install rubber mats all the time, and water gets under them. Unless you have an open scratch in the steel (older trucks), it's a non-issue. My 10 year old bed looks fine.
I bought the impact weathertech bed liner. It is nice and grippy, comes rolled up so takes a bit to get flat. The part attention tail gate curves up, so some reverse bending helps flatten. I've only had it a week, I wanted the wrap around lip as I've not liked 5h3 regular flat mats in the past.
I didn't install the anchors under it because I added a Gator EFX hard cover. I'll never run around with an open bed, and the suction cups seem to have good holding in the bed. It is a unique take on a bed mat for sure, I think it will be great for me.
Was the fit correct by the outlets? A customer that bought the techliner a few months ago stated the fit was incorrect (wondering if he bought a liner for a regular F-150...).