Well, the jury is still out on this - and I'm having a seriously hard time not breaking out my allen wrenches and putting my stem flat again.
Today, I had a local coach/ex-pro do a fitting on my bike in the hopes of straightening out some of my knee issues. The good news is that I'm apparently pretty good at setting up my own seat height/fore/aft and cleat angle - he made some minor adjustments there that felt good, but nothing earth shaking. Did some video analysis, and as is par for most of his fittings that I've seen done for others - flipped the stem up!
This was a serious emotional event for me ( ) since I have modeled my race bike's position after - guess who? Pro Tour guys. Nobody has their stem up unless it's a climbing stage from what I've observed. We talked about it for a while, and my contention that I'd be more aero with a flat stem was countered by his statement that I'd see a lower HR overall while riding slightly more upright, I'd have my elbows bent more, and be more comfortable, and thus produce more power.
I'll keep it like this for a while, and see what happens - but seeing as right now, post knee injury I haven't been able to do any sprinting work - I'm thinking that any success I'm going to see this race season is going to be based on long aerobic efforts...which will be helped by being as aero as possible...I'm still skeptical.
We did a 3 hour slow, base, ride after the fitting, and my average power was 160 - with an average HR of 108. In the past, for longer rides of similar AP, I have seen slightly higher HRs - so there is probably something to be said for more power at a lower HR. I just wonder at what point a few watts saved from a more open position is going to be outweighed by being less aero.