When you do those first few pumps, what little bit of air that is in the line goes into the caliper and immediately goes to the top and out of the bleeder. The air isn't like a single car in a train- it doesn't stay in one place behind X amount of fluid and can't leave until the fluid ahead of it (all that new fluid) is pushed out. Once it makes it that short distance through the hose and into the cavity in the caliper, it's going up.
Now, if you were flushing all the old fluid out the system from the reservoir to the back, then you'd put the new fluid in the reservoir, open the bleeder(s) and let the old fluid fill the caliper(s) on it's own.