I've come up with a new, different, more compact design for my boat junction. Like before, the route taken by the boat is controlled by the door, which can be wired to redstone circuits.

The 90 degree turn is important for aligning the boat so that it will travel straight and be able to flow pass the junction door if it is open. The stream the boat lands in, just after it hits the wall in the turn, must be 8 water blocks long and end 1 block before the junction door.

The junction door must be 1 block lower than this stream so that the boat can touch the water in Route #1 if the door is open.

Glass blocks with signs attached are used to control the water flow patterns while still allowing a player to pass through them unharmed.

My original gravity based boat junction can be mixed with this junction design to create a more advanced 3-way junction.