I was in the same position. In the end I was forced to get a different tonneau cover to make things work. You will need to adapt in order to make things work.
A different cover was the most economical solution for me vs. raising 5'er.
Check out the Tonnopro Hard folding cover. I came across this cover after the fact. What is unique about this cover is that it folds up totally out of the way. There are no tracks or rails to interfere with the pin box. It seems is ideal for use with a fiver.
I was in the same position. In the end I was forced to get a different tonneau cover to make things work. You will need to adapt in order to make things work.
Tonno Pro Cover