Perhaps to each his own. But you still have some misconceptions in your thinking, or are perhaps following an outdated model for the storage of files or applications.
The application can be in one folder (read only to all except the admin - yourself?). Thus, your users cannot overwrite the application with a rogue app (accidently, unwittingly, deliberately, whatever).
The main (individual) ^.ini file (mirc.ini) and any associated script files can be in the user's own folder. When you do "one install", the script files do not have to be available for everyone. The location of script files is held in mirc.ini and customisable - this is the strength of the "-i" command line parameter.
You can still use common script files (only one version needed) which you control - if you wish. Users can create and load their own script files in addition.
I argue that a proper multi-user install and configuration will give you more control and will give your users both better customisation and security than the model you are currently using.
But, as you say - each to your own. I am merely trying to point out some of the better practices that are available, practices that are enabled by improvements in the operating system.