It is very strange because every other autistic student I have ever had does great with warnings. If it is something that this student is not going to want to do, as soon as the warning is given, the meltdown starts.
We do the timeouts in the same room, just in a chair in the "quiet" area with the books and aquarium. He has never scratched or hit another student, but because he scratches or hits whatever adult is within his reach at those times, I make sure he is away from all of the other kids. He can still see all of us and hear the class. Sometime while in "time out" he will start to participate with what we are doing and I encourage him to continue participating. Visual schedules are funny! He hates math. When I show him a schedule with the word Math on it, he immediately points to it and shouts, "NO"! He is so funny that way. We tell him, no math, no computer later. He will usually say no math quieter, I repeat, No math, no computer and he will do his math! He is quite good at math, he just really does not like it.

My son does the same thing (but bites as well, it's awful) and his teachers have found visual schedules to really help his transitions. It doesn't eliminate it, but he gets upset much less when he can physically see that it's going to change. They also give him warnings, "in 5 minutes we are going to switch to this task, okay?" So he can prepare a bit because he does not do well with a sudden switch. Sometimes they use a timer with lights that change if he is having a tough day, to really help reinforce the transitions coming up.
My son also doesn't understand the concept of time outs, he just gets confused and upset because he feels alone. I think it's not an effective tool for every child. His teachers have him do "cool downs" where he sits somewhere and calms down if he's getting upset/overwhelmed, but someone stays with him and talks to him or reads him a social story if it fits the situation, etc. Maybe something like this would help this little guy?