How hard is it to get air out of a brake line?

I know normally if you want to flush out the brake fluid: you open the brake line valves and let the fluid run out by gravity(or vacuum) while you keep adding new brake fluid. When the brake fluid that runs out looks like the brand new brake fluid you've flushed out the old brake fluid.

I asked a mechanic about his price quote and he said it would be $40 for a brake fluid flush, but if I had air in my lines it would be $90. I don't understand this because if there is air in my brake lines wouldn't it be purged out with the old brake fluid as I flush it out? Does air in your brake lines make it that much harder?