My apologies in advance, but I feel it my duty to point out that some on this forum (not me I might add) think that flipping the stem the "wrong" way is very bad OCP practice, especially with aero bars!

I say go for it if it's gonna make you more comfortable. I personally have mine flipped down but only because it's more comfortable for me this way and I can get lower in the drops. I don't have aero bars either.

Hope all goes well and you're happy with your new setup.