The "Bart" thing was something that someone online correctly countered DiDio's lame statement that "Smallville" should only have iconic characters in it. That has never been the case before in the series, and shouldn't be the case now. Miller should have access to every single character he wants to use in the DC pantheon without being dicked around by editorial because they only want to shoehorn and "showcase" characters they want to promote. They did the exact same thing with the series: thus why we got episodes involving Cyborg, Aquaman (Arthur possibly being one of two iconic characters along with Oliver of course), Mera, and "Bart" Allen, oh and I forgot Mia Deardren (even though I was excited to see this version of the character) over Roy Harper. Ollie Queen was basically their abandoned and tweaked plans for Bruce Wayne.
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.