Is it because pamac build from flatpak?
Usually flatpak apps ignore system font configuration (anti-aliasing, hinting, so on).
Why by the way?
All other apps (except pamac) follow my font configuration.
Pamac is from distro. I didn’t install it explicitly.
Try
pamac install pamac-gtk3
It’s not a FlatPak, it’s a GTK4 application, unless you’re using the GTK3 version. GTK4 is very difficult to customize, so perhaps you are better off using the GTK3 version. 
sudo pacman -Rdd pamac-gtk && sudo pacman -S pamac-gtk3
Because they run inside a container, with their own fonts and theme, and they have very limited access to the underlying system.
pacman-gtk? Maybe pamac-gtk.
It was a typo. Corrected now.
Can fonts for flatpak apps be configured somehow?
I don’t think so. I don’t use any FlatPaks or Snaps, so I cannot tell. But in general they don’t follow the system theme or font selections.
What are differences between pamac-gtk (on gtk4) and pamac-gtk3?
Why is the latter better?
It’s a matter of preference. GTK4 is notoriously difficult to tweak, while GTK3 has more theming options. pamac-gtk is more at home in the GNOME environment.
Other than that, pamac-gtk also requires plugins for Snap and FlatPak support, which pamac-gtk3 does not need.
Some more background info:
Can fonts for flatpak apps be configured somehow?
To fix Flatpaks anti-alias font and theme problems under KDE Plasma, simply install xdg-desktop-portal-gtk package then reboot.
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