ftp.isc.org is a site for archiving and testing control messages. It's not
a site you would peer with, so it's not logical to build your active file
from there.
Various newsgroups weren't started with control messages. Entire hierarchies
aren't maintained with control messages. Various hipclones over the years
sent newgroup messages in great quantity as denial of service attacks. Some
of these got archived, but many didn't.
Lastly, Giganews and Astraweb decide for themselves how to present Usenet
to their subscribers. If they chose to create newsgroups that weren't
started with control messages, or to ignore rmgroup messages in
managed hierarchies, that's entirely up to them.
Are you supporting users? Did they have a need for all those newsgroups to
be created on your server that aren't necessarily Usenet?
If you peer with Giganews and Astraweb and you want to present their view
of Usenet to your users, then you're going to want to use their active files.