I know that you can use all versions (the latest being 4.6.1) on systems through Mac OS 8.6. You have to have version 4.6 or later for Mac OS 9.0 and later (I have been using ATM Deluxe 4.6.1 and ATR 2.6 with 9.2.1, both can be downloaded and install using at least the 4.5 license number).
For people using Suitcase, I believe you need at least 9, if not version 10, to run it with Mac OS 9.0 and later.
I should point out that fonts are dealt with at a system level, and the introduction of ATM Deluxe or Suitcase to attempt to extend the system's abilities does introduce instabilities to the system. There are also incompatibilities between ATM and Suitcase that can be fixed by changing the order of the control panels loading at startup (I believe you can find more info at the Extensis web site).