Antergos = Arch + Cnchi
Antergos directly uses unmodified, native Arch repos. Antergos is not an Arch clone. It is the graphical installer - Cnchi - that installs native Arch. Stop.
Antergos has one additional repo - [antergos]. It mainly contains some additional useful packages, not available in standard Arch.
With the default, highest [antergos] priority few packages slightly alter Antergos behaviour relatively to Arch. Currently these are Cinnamon and Mate packages.
The [antergos] repo priority in Antergos may be lowered - it may be placed below Arch repos.
The [antergos] repo may be freely added to native Arch Linux. Above or below the native Arch repos.
There’s no any difference between Antergos with lowered [antergos] and Arch Linux with [antergos] added below native Arch repos. Both are closer to native Arch Linux than to Antergos.
There’s no any difference between Antergos with [antergos] at the default highest priority and Arch Linux with [antergos] added above native Arch repos. Both are closer to Antergos than to native Arch Linux.
There’s no any difference between Antergos without [antergos] repo (it may be removed) and Arch Linux.