I have to respectfully disagree with this. The OS has provided the user with major settings to control their experience, which all apps can or should be aware are possible configurations the user might select. I don't think it's appropriate for an app to decide that a user's preference is "wrong," but rather, that the app should accommodate the user's preference. In my case, I don't actively check Notification Center frequently, so if one of my macros fails, I'd prefer to have a notification left on screen for me to see (Alert style), rather than discover that failure (potentially) days later (Banner style).
I don't think this is correct. For example, right now I have four macros configured to run at system wake. One of them is emitting this message: Numeric condition failed to get text from source. However, I don't know which macro it is (much less which action within that macro), as there's no contextual information provided.
It's perfectly fair to want to keep the manual succinct. My encouragement here is that in general, I think the app could do more to make the user aware of the existence of the log files.