The stock fork tubes are flush against the top of the triple, none shows above. The handlebar mounts right on top of them. Here's a pic:
To drop the forks on the bike, you can get a lowering kit which basically mounts on top of the triple tree to allow the forks to slide up a bit, then the handlebars are mounted on top of those blocks.
Check out this thread for more detailed pics of what it looks like when the handlebar mounts are removed.