I've been running the printer with the oversize refillable carts. The ones that stick out of the printer. The printer doesn't allow for extra ink capacity and reports the carts as empty when they are still almost full. Presumably the printer is programmed to only monitor normal sized carts. Bit of a bind because the printer door is kept open all the time and when the printer shows a cart as empty you have to remove the piece of plastic (which is used to trick the printer into thinking the door is closed) and then remove and reinsert the cart so the arc chips reset to full again and thereinsert the piece of plastic again. No real advantage in using the oversize carts as the printer doesn't monitor the ink capacity in them.
I tried to override the ink warning by pressing the red x but doesn't work on my printer.
As for refilling original carts, EBAY sellers of the resetter state that you can't reset the original carts and you have to reset carts before they go below 15% capacity. Like you say, it's strange about the original carts because Brother would surely use these chips on all their carts