@ motorollin
That's a semi-official SetPatch, so you're in good shape. The Envoy network package even installs it automatically. Personally, I wouldn't mix a 3.9 CPU command with a 3.1 system (just a little OCD behavior on my part), but it's probably fine to do.
3.5 didn't come out until late 1999 and there was loads of 060 software on the market before then so I don't think you need to worry about the faulty autodetection with 3.1 (ShowConfig is also affected). As to CGX, I don't believe there are 060 libs. Just generic 040 and up.