I’m having similar issues with my Mopar hard tri fold (made by Bak). Don’t think there’s too many covers out there fully water tight. Rain gets in up by the cab, need more weatherstripping in the corners. Rain gets in by the tailgate (pics) because the water rolls off the end of the rails into the bed. Rails seem too short, although any longer and they’d impede closing of the gate. Also rain is dripping through the rails onto the wheel well, which must be a defect in manufacturing because there’s no other explanation (pics).
On a previous thread someone suggested contacting Bak to send new rails bc he had same issue and they said it shouldn’t do that over the wheel wells.
I will add some foam at some point as mentioned above (thanks for that) and more weather stripping by the bulkhead.