I just did mine 2 days ago. If the shaft did not mate then ,like you said the casting would not be flush with the block. I had trouble getting those two shafts to line up and I had to try 3 times removing it , turning the shaft to what I thought lined up until it went all the way in and could go no further.
If you look at the two remaining holes and the backside of those holes can go no closer (flush to the block) you are good to go.
When I did not line up the shaft I had a gap there so I knew I did not have it mated correctly. I never thought to look at what you are seeing since it could not get any better than all the way in.
So if it can not go in any further, that shiny part must be normal.