I think I now see what you are talking about.. Here is a pic of my lid and that strip of metal you talk about.
Mine just barely clears, but enough that I didn't even notice it when I installed it.
They must have drilled your handle holes "just off enough" to interfere with that bar, which I don't know what it's used for, other than maybe added structure for the lid??
I'll bet you can call them and get a new lid for your unit.. How long that will take is up to them, but yeah... That sucks for sure!
Mitch
2013 F150 XLT 4x4 SuperCab Max Tow Egoboost 3.73 gears #7700 GVWR #1920 payload. 2019 Rockwood Mini Lite 2511S.