Awesome tank! Somehow i havent seen this one. I dont really have any experience with HC, but i know with my glosso carpet i have going in a ten gallon i had some brown areas and i cut them out and it filled right in. I would assume you'll see the same results with HC. I'm sure someone else will chime in that has more experience with HC. I know with my glosso i trim constantly and it makes it thicker and thicker.
As far as flooding, in that last pic it looks like you have some great root development and depth, i would say your more than ok to flood. I dont run Co2 in any of my tanks, but wouldnt mind trying it. I'm curious, what DIY did you go with?