Maybe you're mistaking the bilge pump for the baitwell pump. The livewell pump runs to both the baitwell and livewell on my tracker, one pump for both wells. The bilge discharge line looks like it might run to the baitwell but it doesn't, it discharges near the baitwell.
Post some pics of the inside and outside of your transom so I can see the pumps on the inside and the pickups on the outside.