Yeah the instruction in the manual doesn't empty the water pump. The bolt where the red arrow points to in the pic is a sump bolt, not on the water pump, btw.
The way to full drain the system is to open the 3 bolts and separate the front cover of the water pump.
Or, if you don't want to upset the o-ring under that cover, you can remove the water pump from the engine and turn it upside down.
A little oil will come out the water pump drive hole but if you put the front wheel up on a 3" block for example, before pulling the water pump out, it will keep oil away from the front of the sump.