That makes sense, and I guess it's closer to the way paintball2 currently works with ammo (if you've got 99 balls in a 100-round hopper and pick up a 200 round ammo pack, 199 balls go to paintball heaven).
The way I had envisioned pod filling, though, was you'd have to hold the reload button down, and the longer you held it down, the more balls you'd load. As soon as you let go, you'd stop reloading and save whatever balls were left in the pod for later, but I guess the reload-till-full-and-drop-what's-left idea would probably work better.