It actually depends on how much “help” you need. If you can get the balls of your feet down pretty solidly, a higher heel will get you flat footed. However, if, like me, your really stubby legs won’t even get you that far, a higher heel won’t do much for you. What will help is a thicker front sole. Too bad I couldn’t get these under my shifter, http://www.wildfree.com/prods/dem-stack308.html.
Personally, not being able to flat foot for me is an inconvenience, but I’ve learned to work around it, and on flat ground it is pretty much of a non issue. When the pavement isn’t flat it can add a bit of adventure to coming to a stop, I’ve had a few moments when I went to put my left foot on the ground and the ground wasn’t there. Never dropped, but a couple of struggles. All in all, I wouldn’t let seat height be THE determining factor in your choice of bike, A factor yes, but a high seat height is something that can be overcome with, like everything else we’re learning, practice and repetition.