The Street 500/750 aren't really cafe racers that typically use rear controls for the lay-down road racing style of rider position. At the same time they're not a cruiser either. They're that in-between motorcycle for normal street use like the older mid-size motorcycles of the past.
Possibly adjusting the motorcycle with a different seat and handle bar combination for comfort in riding the Street 500, as with any motorcycle, is always advised and I believe you've taken good pragmatic steps in addressing that. Rarely does any motorcycle "fit" perfectly from the factory based upon my personal experience and I've always made minor tweaks to address that including seat changes and handle bar changes if necessary. I've also moved the foot controls because they just didn't feel right for me.
My point would be get it the way you want it because you'll enjoy it more because of those changes.