If I'm following you correctly .. then Yes .. you could cut the longer top bracket, as the connection to the rail is at the bottom of that top bracket .. so it ends up at the exact same position as the smaller bracket. Both the short and the long butt up aganst the top of the lower bracket. As far as I can tell, the only reason for the longer bracket to extend the coverage higher to cover any holes that may have been there from the previous install. So, to cut that down, smooth the sharp corner a bit so it doesn't catch on anything, cover the cut with some black paint and drill new mounting hole near the top if needed shouldn't be a problem.
As discussed above, I think the way to go is to cut the long bracket to custom fit what you need to cover the holes and stay below the awning.
I figured that worst case scenario, I was cutting the bigger bracket.
