Those 3 groups  are only created in the Top level site  of the site
collection. But as with all SharePoint groups they are meant to be
available in case AD groups don't exist or SharePoint admins  don't have
Domain Admin authority. In general you can continue to use AD groups to
manage SharePoint.

There is one compelling reason  to use the Site members  group. Some of
the webparts, like the My sites  webpart in you mySite, key off
membership in that particular group instead of a wider check of
security. In other words, if you are not a member of the Site Members
group of a particular site then it won't show up in the Sites List in
your Mysite even if you have security rights to the site.

> There is one compelling reason  to use the site  Members group. Some of
> the webparts, like the My sites  webpart in you mySite, key off
> membership in that particular group instead of a wider check of
> security. In other words, if you are not a member of the Site Members
> group of a particular site then it won't show up in the Sites List in
> your Mysite even if you have security rights to the site.

So, to use that properly, one should have a member group for each of
their sites, correct? I'd be OK with that, but it just seems 'messy' to
have groups  for every site that people  have to wade through.