silicone isn't permanent, you can just pry it off if you use silicone. silicone is always pliable, so you won't be as rigid. i wouldn't use silicone if your goal is rigidity.
with the adhesives mentioned, you'd make it stronger. MDF is waterproof once coated in resin. it's also stronger at that point. A good 7-ply or 12-ply birch would be stronger than MDF. I wouldn't waste any time on wood thinner than 3/4".
note that the roof line will vary. i would make a cardboard template for each section, maybe you can reuse the same template a few times. cardboard is the best way to get a template without wasting wood. Note that when tracing cardboard cutouts the lines won't be perfect. I use the cardboard as my first pass, draw lightly. then i go back over with a straight edge to make the lines nice and smooth. if you don't, you'll end up with a jagged piece of wood from following the cardboard trace.
when you attach the roof boards, recognize that they will be the new source of flexing, and should be fairly strong. i would keep a perfect 12" or 18" between braces. then you can cut out some 12" or 18" strips. those strips would fit tightly between the roof braces to offer more surface area for the roof and more rigidity.