See @Kiwih answer.
Apps appear in the list when they effectively communicate through the network, in the concerned period of time (day, 7 last days, since installation). If you are sure that an app has communicated through the network but it does not appear in the list, that’s a bug.
Some system apps already appear (e.g. intent verification filter plus all preinstalled apps), but many do not appear indeed. They are filtered through the “Standard” black list though. We don’t want to flood the app list though, so we plan to make them all appear into a single aggregate app called something like “Android System”.
This is an interesting idea, we will think about it. We are however working on a new feature, to block network access depending on the network interface (wifi, mobile data, vpn), as well as defining default blocking state for newly installed apps. This is a bit redundant with android settings, but more powerful: it will be for example possible to allow blocking wifi and mobile data while still allowing vpn, regardless of the way the vpn is connected (wifi, …).
The whitelist principle for domain filtering could also be explored, we have to think about that.
We plan to integrate more the blocker in the overall user experience, to better interact with it. We will probably display some real-time data, and internet access may be one of them.