No Aeliss, this is not a portable version and, that's right, the previous 'system.xml' file would be overwritten.
I remind you that there's an "Export" button in mGalaxy_Runway. This will pack all your mGalaxy settings in an auto-extractable .zip file. You could then try the new version, make some tests, then un-install it and re-install the previous one. Then a double-click on the .zip file would restore your "old" settings.
The 'system.xml' file is overwritten when new major functionalities are added (such as database support for all systems, coming with the new version).
I'll try to work on an updating function of that file in the future...but in the meanwhile I could just advice you to save your "old" 'system.xml' file in a safe place, then do copy/paste between versions!