not sure if that would be appropriate for the Cookie app to be able to handle this, but please try to have a look at it if it would be feasible...
As You know, there's a new API for content blocking extensions since Safari 9.0.
Extensions that make use of that API don't seem to store their data in the usual browser local storage (which Your Cookie app can manage), but in the following locations instead:
AdGuard Browser Extension https://github.com/AdguardTeam/AdguardBrowserExtension/releases is one such example - it seems to generate and store its blockinglist into the above mentioned location and then uses that together with its settings which are stored in:
e.g. storing nothing in the browser local storage at all.
It would be nice to be able to manage that stuff in Your app as well.
Some possibly interesting resources regarding the content blocking API:
Yes, currently only ad blockers it seems, though the author of the JS Blocker extension said he may consider using that API in the future (if the restrictions of the filter list size - currently 50000 entries AFAIK - are improved).
I just posted a beta with support for ContentExtension data