I think you have outlined very well the reasons for using the adapter plate.
However, your statement
"The third reason is that if you need a new water pump, then you can just simply bolt the new one on instead of modifying another one again." is a simplification.
If you use the plate, and you ever have to replace the water pump, you cannot simply unbolt the old one and bolt on the new one. The plate comes off with the water pump and would have to be attached to the new water pump (which is not a difficult matter; but, it is not simply a bolt-off and bolt-on of the water pump).
