[hypoxia]

Methinks the "Mystery Bypass" is just a manifold.  The brass fitting on the left side of it is a check valve to prevent backflow to the 12VDC pump.  Good chance the check valve is seized with deposits.  You can disconnect the hose going to it & see if water flows from the check valve.  That valve is spring loaded with a snap ring.  You can remove it, take it apart to soak it in vinegar, replace the "O" ring and make it like new again.