This is interesting from your perspective. I think you'll appreciate the S a bit more coming from the 2.7 vs. someone who just got into the S to begin with.
I already had very excellent handling but modestly powered Miata before getting into the S. My first reaction when I floored the S was
I've driven the 2.7 and from my perspective it is a big difference. A bigger differnece then I noticed driving a 3.4 vs. 3.6 911 (2002+).
I remember reading an interesting Excellence (late 2004) article "Best Porsche Convertibles" and a regular contributor wrote (pre-Cayman/987)
"The Carrera GT and BoxsterS are the best handling cars Porsches has on offer...The BoxsterS delivers everything the Boxster promises". Strong words.
At local autocross events I've regularly matched the 996's and I'm always quicker than the 993's. Sometimes those 996 and 993's are driven by very good drivers so I'm thinking the extra displacement helps for sure.
IMHO, The six speed gear box is much nicer/sportier, the brakes are better, two radiators, more torque, upgraded suspension, it all adds up. And when you merge onto the highway or overtake a slow poke you'll really appreciate the 258 HP. I think at this weight, a sports car should have at least 240 HP. To me it seems to come 'alive' at that power to weight ratio. At 330 it would be a dream.
Also does the S your considering look newer? That might be another reason to go for it. Interior wear counts for allot to me.
p.s.
aftermarket glass tops are available for all Boxster model years.