I'd drill around or notch them just enough. The fronts are very important and a paint to adjust with the cover on, so make sure it's perfect before you notch. As long as you don't compromise the bracket all is good, however, as long as you have low profile plates for the hooks, you may not need to notch at all, just put the clamp over the plate.
Steel horse/VDP used to have some really nice pieces that replaced the stock covers and would only need to be relieved so you could move the hook up and down.
The nicest divider I have seen is Loading Zone's,
Loading Zone - The Original Cargo Gate
It has a cam'd side that releases with a flip of the handle, but they were getting too expensive the last time I sold one. Keeper makes some cargo dividers, ratchet and shower curtain style.