Water Pump Help Please

Got it timed and belt off just the water pump to come off I've undone and removed the 5 bolts but it appears to be stuck where indicated in the photo, this hole on the new pump is threaded. Have I missed something I thought this hole was for a locating pin so why is it threaded? another model perhaps. Thought I should ask before getting heavy handed and forcing it.
The bottom right mounting point on the new pump is also different and has what I believe is an evaporation chamber and I can understand what this is meant to do, what I can't understand is why does the mounting bolt have another 8mm bolt screwed in the end which in my case was literally finger tight it appears to do nothing.

There is a bolt that goes through it from behind.