Are you sure that auto action is what is causing the emails to send? Try unpublishing it and see if those emails still send. You may have something else sending those emails.

but if we go that route it won't prevent the other members getting notifications logged for groups they aren't part of right?

Again that notification only sends to members of the group. I suspect you've something else causing emails to send to everyone. Will retest this tomorrow, but it was extensively tested already.

I've retested CB Activity > Notifications > Activity > Create (Group) and seams to be working perfectly fine in my tests with Recipients set to Group. It only notifies the members of the group I posted in. Notifications of course exclude ones self as notifying yourself about your own post is a bit strange. Note the recipients need to have "Create of new post" set to "Yes" under the groups notification page as well.

It sounds like you've auto actions still logging activity and that's where all the weirdness maybe coming from. Did you unpublish your custom auto actions? If not those are still going to work because the save triggers did not change. If the system actions still exist run Reinstall System Actions in CB Auto Actions > System Actions so it can delete those.

3 - Posted comment on one of the posts

There is no group specific notification for commenting on group posts. Post comment notifications notify the post owner.

I don't know what more to suggest. I've retested it several times now and works fine. The only reason for everyone to be notified is if Recipients is set to All Users. Please PM backend super user login credentials and will take a look at your configuration.