Good points, but you also have to think spending 4 years at a time trying to peak for one event is a hard thing to do mentally. Also, for Phinney, personal glory definitely wouldn't be near guaranteed with no IP (or Kilo) in 12/16 games. His best bet would have probably been TP, but that's putting a lot of faith in finding 3 other prodigies. Keirin possibly with the right focus, but both it and even more the omnium require a healthy dose of luck as well as skill.
Hoy was obviously brilliant (as well as Kenny) but when we compare the two we really just go right back to the culture surrounding the athlete. Big difference from 2008+(04 really) in GB and the USA. My guess is Phinney likely would have been lucky to medal. Not to say that his road career has been easy either.
*speaking just in terms of Olympic medals. If you count WC / big events, it's almost a sure thing Phinney would have been VERY highly decorated.