Hi Martin, yup you can run the .app from wherever you want, it doesn't have to be in /Applications, that's just basically a convention to have them there.

The different versions will all share the same moi.ini file for settings, the default moi.ini file will be located in your user directory, under ~/Library/Application Support/Moi/moi.ini .

It is possible to have each one have a separate moi.ini if you really wanted that for some reason, to do that you would need to make separate moi.ini files for each different one and set up the path to the .ini file as a command line parameter, there's some information on how to do that for MoI on OSX here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4675.8

- Michael