Ahh, now I get it.
We have not implemented this for two reasons:
1. The interface of League of Legends isn't as quick as AutoLoL and it's very hard to determine when it's ready. So it's very possible AutoLoL presses save when Leugue of Legends is still busy.
2. There is still a possiblity of AutoLoL making an mistake. Leaving the window open gives the user a quick chance to review their masteries before saving.
Hope this clears the issue.