It's not just the lack of blonde hair (which I don't think was completely off the table), going with a short hair lends itself to a more "Superman" look, and Supergirl's costume while inspired by Superman generally looks distinct because of the skirt or dress, and I don't think they didn't include the skirt because a certain section of people feel it's problematic (from the same studio that gave Wonder Woman and Mary Marvel a skirt).
And on-top of that she's getting the Flashpoint Superman backstory with an actual Superman nowhere to be seen, unless you believe the Cavill rumors.