It must make it more aero - you've got a frame that's, say, 700mm bottom to top versus one that's say 750mm bottom to top. With the taller one you then still have a stem on it but it's -17 or whatever to get rider back into position. The taller frame is always going to have a greater frontal area. I've never used a handlebar bag. I try and get most of my stuff on the frame or out the back rather than on the bars.
If your stack (at the bars) and BB drop is the same between the two frames then theoretically the frontal height is exactly the same. As long as the sum of the stem angle + headtube angle isn't greater than 90°.
It must make it more aero - you've got a frame that's, say, 700mm bottom to top versus one that's say 750mm bottom to top. With the taller one you then still have a stem on it but it's -17 or whatever to get rider back into position. The taller frame is always going to have a greater frontal area. I've never used a handlebar bag. I try and get most of my stuff on the frame or out the back rather than on the bars.