Does the choice of peppers affect the 'flavor of the heat'?
The heat is the same; all peppers contain capsaicin. The Scoville scale defines heat in terms of capsaicin content. Use the peppers that have the flavor you want, and make it as hot as you want, and you'll be set.

And the flavor besides heat is definitely concentrated in the flesh, so you shouldn't notice any real difference in pepper flavor either.