The center brace is not an issue. You should remove the glass tops (not for the light, but for better gas exchange on your SW tank).
You can adjust the optics on the LEDs if you are concerned about them penetrating to the bottom of the tank. I don't see an issue going with the standard 90 degree optics that come with the Photon units. I have 2x 32" photons on my 125g. I have no issues with the two center braces I have and I believe that my tank is 22" deep, corals on my sand bed get all the light they need.