If you put a Mob in a boat, to try and remove the Water in a boat, the Mobs legs will also be removed as well. This issue doesn't effect Players, but seems to effect all other Mobs.
Mobs will fully render sometimes, but water will go into the boat as well.

Pic 3: A simpler way to make Water not render in Boats, might be to do it in a similar way to Enderman Glowing Layer or Spider Glowing Layer. Transparent parts of Mobs will Un-render Water.