Yes the cup and flag are visible to line up your put,but when you strike the ball the cup and flag are no longer visible. it would make the next put easier if you could have seen the roll on previous shot.
On some of my missed putts - not many, but some - I've seen the view cut away to a close-up view directly behind my avatar. Basically, a giant image of my avatar's forearms and thighs that blocks the view of the ball as it completes its roll. Is that what you're talking about?