... gear leaver and break lever were significantly lower that pegs where we keep our heels. I was expecting them to be in line so that my feet would have stayed in almost horizontal position.
Well, you should have the balls of your feet on the pegs, when not operating the levers.
On a sporting bike, it's the norm to have the toe pegs to be a good bit lower than the foot peg. If you take a look at the site stopintime liked to - you'll see that unless you have a really short inseam (so short you cannot put a foot down) you would need to flex your foot a lot to operate a lever with it's toe peg in the same plane as your foot peg. Sufficient flex you might not be able to do it, or at least do so comfortably.
The shifter on my 900 is about 1.75" below the pegs. About the same on my Super Moto
Either way, it's easy to adjust the positions. For the shifter, big moves need to you to move the short arm on the splined shaft a notch. Fine adjustment are done via the connection rod. One hemi joint is normal thread the other is reverse. So you loosen the choke nuts and turn the rod to alter the length which will move the toe peg height. Different method, but similar concept on the brake side