Ghost switched recently to making those error messages more prominent. That looks like a nuisance error (who cares if the theme sets a variable and doesn’t use it?), and possibly a mis-reporting (some variable use doesn’t “count” for deciding if the custom setting has been used). I’d ignore it.
Here’s why I think flagging this error is important:
A theme developer adds a custom setting:
“Change post layout.”
Grid
List
Masonry
But they don’t actually implement the setting in the theme. For the user, then, they would be changing this setting but not seeing any change in the theme, which would be frustrating. This error warns the user that this setting won’t actually do anything.