I thought the dimple was a couple inches above his flare's screwhole? either way, the easy solution would be to lightly mount the flare with the existing holes, jab the cover with a nail or something, install the clips, screw everything together. That's what I did, took maybe 20-25 minutes with my Leatherman Micra. Would have been 10 minutes if I had my little right angle allen tool handy. The dimple won't bother anything, it was there before you installed the flares.
That's assuming the flare lines up properly otherwise.