We thought about using standoffs, but we are trying to keep the retail price bellow $24.95usd and standoffs are a bit expensive. We buy most of our supplies from McMaster and the 4-40 standoffs are around $1usd each.
We decided to machine the standoffs into the case because we can actually shorten the height, to 0.15" and decrease the mounting hole platform radius to 0.08" as oppose to 0.11" for the smallest 3/16" brass standoffs, while reducing the cost. With 0.15" of bottom clearance and .08" mounting hole platform radius, we haven't encountered short circuit problems with the Uno R3, R2 and Duemilanove boards.
However, you are right regarding the crowded component placement on the Arduino board. On the R3, the hole closes to the reset pin is right next the a couple headers, but we can easily secure the R3 using the other 3 mounting holes.