I have the Retraxone MX and noticed the same thing. I had it installed for me a week ago and wondered if they had trimmed it too short but saw your posts and it looks like its coming from the factory like this.
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I bought some weather stripping to try and seal it off for now. It works ok. I took it through a touchless car wash today. I have a carpeted mat in the bed and it was slightly damp in the corners near this point on each side, but also at the corners by the tailgate. I'm going to send a message to retrax as well and see what they say.
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