The plane of the cutout is still flat.
Start a bit smaller than you think, can always make the hole a bit bigger.
For sealing best practices are from the marine arena, building new and fixing old boats. Some do custom port lights just a plain sheet of "glass", fixed in place to withstand huge pressures for decades, lives at stake
Bed-It is the best butyl, plenty of "give" to securely fill a varying width gap, stays flexible forever.
http://shop.marinehowto.com/products/bed-it-tape
Don't clamp it too much squeezing it all out, let it "seep" 24-48 hours then tighten up a little more not too tight. Some embed a rigid bead to ensure the desired gap.
A more modern paintable sealant can skin over cover the butyl if you want, but must also be a permanently flexible type, usually urethane. Make sure not so adhesive that you can never re-bed if needed, permanence is not the goal.
Before I make a mess out of my roof with this stuff (MaxxAir install) I am curious if there is another cleaner option that is as good. Any sugestions are appreciated. I know you cant really see the roof. My bedroom window looks right down on it though, lol. I considered making a little dam...
sprinter-source.com
Does anyone have experience using this product on a boat ? I got a piece of it from someone in the yard and it seems very similar to the putty used in my hull - deck joint and binds well to butyl tape.
www.cruisersforum.com
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Also seen 3M 08609 Window-Weld Super Fast Urethane recommended from the RV world, comes in black