You're confusing two different issues. The first (the first two links, and the one you linked to Jon commenting on) is how minimap scrolling should work. I'm OK with how it works.
The second (your third link, i.e. this thread) is inconsistent behavior when refocusing the window. Suppose that I have two applications open, Sublime Text 2 and Opera. I'm looking up some documentation in Opera and want to go back to ST2. I click on the ST2 window.
If I click in the text area, ST2 properly refocuses and discards my click (since the click was only meant to bring the window to the foreground).
If I click in the sidebar or the minimap, ST2 refocuses and then processes my click, sending me to a different part of the file I'm working on, or possibly even a different file altogether. This is deeply undesirable behavior and gets really annoying, since the sidebar and minimap are on the left and right edges of the window, and thus the most likely parts to be showing behind another application.