I had a similar situation with one of my sons- What I did was"name" them 2 separate events, one being time out, when behavior warranted a cooling down time, and the other was called "quiet time" where he wanted some time alone and he could do a quiet activity. He quickly was able to distinguish between the 2, and to this day (he's 11) will ask for "quiet time" when needed. Good luck :)
Kelly