Also realize that the boat tails are generally easier to reolad, due to the tapered base entering the case mouth. That said, in short action cases, I am reloading almost exclusively flat base as I am just not comfortable seating those long ogive bullets that deep in a small case in order to get the overall length right. In response to the original question, the differences I have seen on velocity between flat base vs. boat tail (IN THE SAME BULLET) have been marginal across my chronograph. However, some boat tails (ie ballistic tips) generally are much faster.
Smoky