I feel like we've just entered another discussion entirely.
What does your example of multiple ON INPUT scripts have to do with the builtin Alt+O options in mIRC? Options tend to have little effect on such scripts.
I'm still not exactly sure what you're trying to do, or why having scriptable access to the options dialogs are necessary. If users do need to change options, they should be doing it from the Alt+O dialog. You shouldn't be making new UI's to configure this-- that just make things *more* confusing.
Maybe I'm just confused about what your goal here is. If you believe that programs where everything is command controlled are difficult to configure, why are you asking for *more* commands to configure the program? This is really confusing. Maybe you should start from the top and try to explain this properly.