Top fuel has to run a certain bore spacing, 8000 HP requires a certain cylinder wall thickness to live, hence the small bore. It is as big as reasonably possible within the rules. No specified limit directly on the bore size but the block is the limit. Same with pro stock, bore spacing is limited so in a way so is actual bore, you just can't run a .010 wall between the cylinders. Both stroke to the max (allowed by the rules) displacement after they settle on a bore that will live.

You are right on about R/S ratio as for how it works and the benefits but I think displacement trumps it to a farther degree than most would think.

Also there are not huge frictional losses due to long strokes (unless you try to run the same RPM), they just run lower RPM through gearing and friction is then basically a wash.