George, CEO of Honey here.
Thanks for bringing this to our attention. Happy to clarify everything here.
The screenshot OP posted shows a registry value in the location "\software\microsoft". This is not Honey because 1) browser extensions cannot make changes to registry value and 2) we do not support Microsoft software at the moment. So what OP observed is not at all related to Honey.
Regarding the YouTube flag, it's because the link OP posted is the redirect URL with an expired token. If you go to the YouTube video at: https://www.youtube.com/watch?v=JnZM9VY86_w and click on the link in the description, it will not be flagged.