As a general note, we tried to avoid modal dialogs as much as possible
Whether it is modal or not, a dialog or something else, doesn't really matter to me. There just needs to be a confirmation that the user understands the potential for making an extension operate incorrectly.
A bonus step (and now I think of it, we should just do it as well) would be to change the setting to user-set, so the extension would be properly notified that it no longer controls the setting.
I guess it's about someone modifying a preference (by own initiative, by following a tutorial, or by recommendation) that will later be reset to a different value anyways.
No, it's about changing a pref that an extension currently controls. If a user tries to change that in about:preferences, the ability to change it is locked out. The user can regain control by disabling the extension (soon, for some settings, it will be selectable). If a user changes something in about:config, there is no indication that an extension has set the pref. Changing it could have side effects for the extension, the user should be aware of that when making the change.