I have two ego twists purchased from the same vendor, one was a replacement that I received about 2 months after I purchased the other. I ordered two T3s from the same vendor and they do not sit flush. I account this to the center pin on the T3 hitting the center pin on the ego before the base sits flush. The newer battery has a slightly larger gap than the older one, enough to fit a thumbnail in. If I look at them closely side by side, the only difference I can see is that the center pin on one battery is slightly higher than on the other battery.
I do not think that this has any affect on the draw of air through the T3 because the draw is limited by the diameter of the hole in the center pin on the T3. If the draw is too loose then the center pin on the T3 would be at fault as this should be the limiting factor on any clearomizer. The batter should not effect the draw in any way in my opinion.
Edit: I'm not saying that the battery does not effect the draw, but I don't think that it should...the threads may be covering up the air holes leading to the outside of the T3 base giving some a tighter draw.