Frustrating indeed. Good luck.
While the EPDM would have been waterproof achieving a strong lasting bond would have been difficult.
I would recommend somewhat generous pleats between cab and camper to allow for chassis flex, but not so big as to allow aerodynamic pressure when rolling down the highway to suck on fabric, make it flap and thus over-stress the bonds.
Waterproofing the hatch and tailgate will be it's own challenge. Dry bags and tarp wrapping bedding may still be necessary in the monsoon season.