Personally, doing the -r \path\mirc thing is not really a big deal, but it is a nuissance just the same.
One problem I see is how to install additional mIRCs. If the user can't choose where the data files are stored, then each new install of mIRC will overwrite the existing files in \application data\mirc. I still think an Advanced Options button is an ideal solution. Ordinary users can install to \program files\mirc & \application data\mirc without choosing a single path (default paths provided by the installer).
Maybe get rid of the automatic serial number idea, and leave it to the advanced user to choose the program and data folders manually. It seems quite simple to me (even to implement). When I upgrade/install each mIRC on my PC (I have 3 on this PC), I simply change the install dir to \mirc1 or \mirc2 or \mirc3. It would be easy to put that dir on the end of 2 paths instead of 1. And once the program is installed, instead of a whole data folder management dialog, there would be a textbox and a browse button to let you change the data folder location.