It's possible Goyer's "Flash" movie was the true reason...but no one really knows why we got Bart instead of Barry. At the time many of us theorized that it was a younger time traveling Barry Allen who used his name as Bart.
But Bart is still Smallville's version of The Flash, correct? You don't think that they're going to try to introduce a different version at this point, do you? I would think that if Miller basically has the freedom to pick and choose his material and/or characters, then we could see Bart change his name to 'Flash' inasmuch as Clark went from being the Blur to Superman.
Just my .02 worth.