The 'pre' commands execute before the connection is even started. Can't think of many times you would use it . . . pehaps if you wanted to kill other connections before you start this one, clean a temp directory you wanted to use, start some kind of logging software . . . guess it might have a use.
Thankfully, the connection manager takes care of the negotiations. Not fun the old way.
The error handling that I was referring to . . . if you were to set connection manager to run a script hosted on the server, there isn't a good way to deal with a situation where the script is not available. If you write batch file to include with the connectoid, you could make allowances for the remote portion not being available. Not a big deal, but that is why it is configured the way it is. Hope that makes some sense.
On another note, there is a new version of the CMAK included with service packs (starting with SP2). The files are different, but I'm not sure what has changed. At any rate, I would use the one from the SP.