If mIRC.ini is in the mIRC folder, that is the file that will be used for settings. I'm not sure what happens if you do that in Vista since Vista doesn't let you write to the Program Files\ folder. It does work as expected in XP and is a good thing to have for those of us who prefer to keep everything in one place. If you don't want to use Program Files and/or you're on a single user system, it is much easier to just have everything in a single folder rather than trying to jump around into appdata folders. It also makes is much easier to create a single backup file for mIRC+settings+scripts. Otherwise, you have to backup 2 separate folders and then merge them. A waste of time, imo.
As a note, the backup procedure may back up or reload from the appdata folder instead of checking for mIRC.ini. I'm not sure if that may have been missed when making 6.3 and I don't have Vista to test on.