When you install a ROM, all default apps are system apps. When you install a custom ROM and flash GApps, those Google apps are system files. So do you have any idea what any of those are doing? Not sure I understand what you’re saying other than system apps may be doing things you don’t know about. According to AfWall, there are system apps that can access the internet, like Gallery, so we really don’t know what’s going on.
Regarding YouTube Vanced, the root version has the same package name as Google’s YouTube. It’s a replacement. Other than adblocking and other extra features it does nothing differently. It’s still YouTube, good or bad.
The non-root version of Vanced has a different package name and is installed as a regular user app. Either will work fine without a Google account.
I personally don’t use Vanced on ROMs that are Google-free (no Play Store) but on my microG ROMs with Play Store, I use it.
As far as making sense, it’s been said elsewhere, what folks do after flashing /e/ is their business. I’ve said before, if /e/ wanted to be truly Google-free it wouldn’t use microG at all, just UnifiedNLP (which I do on a few which is quite cool).