Since the
engine is probably new, I'm assuming the stern drive is new too. The bravo 2 comes with its own
cooling water connections for the
raw water pump. Normally those are the only cooling connections for the
engine.. I'm guessing the thruhull and strainer was for the old engine / outdrive.
I think it was done that way with the bravo 2 to insure water
delivery to the engine when on plane. I'm betting (I bet a lot is seems) the stern drive has slots/strainer in the stern drive water pickup.
Me I might repipe the Bravo 2 connection to the inlet side of the strainer. Though check with the engine / stern drive manufacturer first, as the old strainer might not even be needed now.
From a hydraulic standpoint water will always seek the lowest pressure path in a parallel piped system. So the water will always flow via the stern drive, due to the higher pressure drop of the strainer.