Notwithstanding Personal Prefence, everything you have mentioned can be achieved more efficiently with the command line parameters.
Here is how I start my second instance of mIRC - totally different scripts and nicks (could even be different networks if I wanted):
"C:\Program Files\mIRC\mirc.exe" -iCCA_mirc.ini
"CCA_mirc.ini" is the additional mirc.ini file.
I currently start in (based on how long I have been using mIRC, and that I haven't done a clean install of the latest one.
But this could very easily be a custom folder - perhaps in teh users own documents area.
You can bundle the scripts and ini files into one place. You can also link to script files that are common between instances (thus, a change in one means a change in all. You can have the best of both worlds.
Releasing the scripts to the public is easy, because you then only have to release the scripts and not mIRC.exe. You can put a shortcut in the individual script folder 'Copy this to the desktop".
Obviously, how you do it is your personal choice, but I think that other readers of these forums should be aware of a more effective way of managing the application, instances and scripts than the standard reply of "oh, just install another version of the application" if they want to run different scripts-nicks.
Running different versions for development purposes is whole different ball game.