It really is a great point. That's why i'm contacting custom car modification shops rather than metal mod shops. If you're interested, google Shaq Jeep - they made a 4 door into a 2 door for him! Anyway, I think a reputable custom car garage should be able to make sure its up to standard.Removing foam from the seat bottom, replacing it with a different density, or even 2 density layers, might give you that 2-3" needed. Welding/ altering seat brackets could be a safety / liability issue
There was a post somebody made on here about removing foam from the seat, he said if he had to do it all over it would have just left it as it was. I'll see if I can find those posts and maybe ask him why he said that.
SIde note - just installed rubi rock rails on my bare (2 day old) Sport S today !