To answer your question (not a dumb question at all, by the way)... The best suggestion that I can give you for a work-around today is to use the "Explore first folder" and "Explore second folder" context menu options to open Windows Explorer to the parent folder of the files you are comparing. This will let you change the readonly file attribute from there.
IDM's mindset when they wrote UC was to prevent users from "shooting themselves in the foot". In other words, UC strictly adheres to the read-only file attribute. Now, your guess is as good as mine as to why the current feedback to the user is so obscure. Email IDM and ask for a better message if you want to see it change. If you want to be able to override the read-only file attribute, ask for that to. The more people that ask for an enhancement, the more likely it is that IDM will implement it.
I've been providing feedback to IDM for years on UC. I've already advised IDM, along with dozens of other enhancement ideas, that any file management/compare utility worth its footprint on an IT professional's hard disk must provide a way to override the read-only attribute--whether that be via an application-level configuration, a Session setting, a "File is read-only. Overwrite anyway?" prompt, or even access to view and modify file attributes from within the application.