If you are planning on filling while underway, I would be concerned about robbing the cooling system.
Also, there is a chance you will always be filling while at speed. Let's say you empty the bags and are headed back. While you go, the water is coming thru the scupper under pressure; some of that may be diverted through the fill pumps and into the bags. Aerator pumps will let water flow through even if they are not on.
Every system has pros and cons. Personally, I would rather have a dedicated thru-hull with its own shut off valve.