Whether you call it a problem or not, it is clearly due to invision. My opinion is that it is a problem, and therefore, I would call it an invision problem. It's one thing to allow settings to be changed from an extra place, but it's something else entirely to overrule settings changes made elsewhere. It should work with mirc's own internal options dialogs, not against them. Having done volunteer mIRC tech support for 7 or 8 years, I know how difficult it is to help someone when you have no idea what their script is doing behind their backs. Telling them to go here, and change this option doesn't work when their script says "no." Sometimes there is nothing that can be done other than telling them that we can't help unless they ditch the script.
Additionally, to say that something is common does not make it right. I won't bore you with examples. If you don't want to call it a bug, that's fine. Just call it a "hidden feature," and maybe we can all move on to problems that are caused by mirc.