I have the Bakflip MX4 as well and would give it three thumbs up if I had an extra thumb. I've run through car washes and other than a few drips in the bed, it keeps things inside dry. Nothing can truly keep a bad guy out if he's got his mind set to it, but for the "average thief" it's probably not worth trying to break into.
Shortly after getting the MX4, I put a Bakbox in it and am really happy with it as well. Yes it eats up a bit of the bed, but it doesn't extend any further than the Bakflip cover, and chance are you're going to put a bunch of junk in your bed anyhow to haul around JIC so I figured why not make it more organized (and blow close to $300)....
https://bakflip.com/bakbox-2.html ---- their website gives much better explanation than I can, plus great pics and video.
Both are great products.