I found that the canopy needed a lot more trimming than expected or initially called for in the plans. The bottom flange (if that is what you are talking about) ended up little more than 1/8" thick. However, beware the angled bracket at the bottom front of the door fuselage frame which can bind the whole thing (sorry, away from home and the part numbers aren't to hand). I actually trimmed away too much from the canopy at that front bottom area. The nice thing about fibreglass is that it's easy to repair it later with some release film and flox once it's in position. To be honest, I was dreading the whole experience but it ended up a lot quicker and easier than I expected. A diamond cutting wheel on a dremel and a flap wheel on a grinder helped no end!
My next job is to fit the doors. This looks like it will entail lots of fitting/trimming/fitting/trimming etc. I suspect that it may be easier to slightly over-trim the door and then build up the canopy sides to fit, again using release film and flox/filler.