Originally Posted by
Jeff Wills
Don't cut them down. They need to have a little height to stay in place if you lose pressure, the tube slips, and the valve tips over.
A friend had his Presta rims drilled for Schrader valves- his theory was that if he had to buy a spare tube at Wal-Mart (he rode a lot of self-supported tours), he could always use a Schraeder tube if that's all they had. I live dangerously- all my bikes have Presta valves and undrilled rims.
Your friend who drilled out his Presta vale holes to Schrader size has some insight, I have to admit.
If the Presta valve was threaded, and you had the nut cinched down to the level of the rim I can't see the valve stem going anywhere even with a flat.