I just went through this exact problem so thought I'd chime in. I have Ram Boxes and MFT
which make the tailgate much thicker and curved so finding a quality bike pad that would protect the bikes, the tailgate and could be made to work was tough. I ended up ordering the Yakima Gatekeeper (
Link) because it is super high quality and has fantastic downtube protection for the bikes.
When it arrived there were 2 issues to overcome. 1. The 1st and 6th downtube protectors on the bike pad were hitting the rails on my tonneau cover stopping the tailgate from closing. and 2. The retaining pin / latch holes on each side for the tailgate were covered by the bike pad.
Solved the 1st problem by taking a Seam Ripper and taking off the 1st and 6th down tube protectors since I only have space for 4 bikes with the ram boxes they would've been useless anyways. Solved the 2nd problem by taking some cutting pliers and making a notch for the pin holes on each side so the tailgate could latch properly.
Works perfectly and I am super pleased with the Yakima Gatekeeper. Best bike pad I've ever owned. Pretty much any bike pad with the Ram Boxes or MFT will require some modification, but it's just the nature of having all of that stuff. Hope that helps!