The two CAM programs I've used to date allow me to specify tool numbers for every OP. As long as the ATC slots are numbered in an easily visible way then that would work for me.
I will say that I don't have TTC and need to measure tool height on every manual change (I have an NM200). If I were to have a Torus with the ATC AND more tool holders than ATC slots, then obviously I'd need to think about mapping, or else modify the tool table in the control each time.
I'd add that the only reason I'd consider selling the NM200 to replace it with a Torus is if the ATC were available, so keep on keeping on.