Most extensions use the convenience.js that originated from GNOME's own extensions for initialisation of locale and schemas. Caffeine's lib.js already provided functionality similar to it, so porting to convenience.js is a small step that simplifies the code a little and allows to follow updates from upstream.
The "Cannot find application for window" message appears quite frequently in JS LOG output, indicating that this is a normal occurrence rather than an error state. Further, the message provides no actionable information, and therefore serves no purpose.
This than be disabled in the extension preferences Ref #20