I use some apps built with Kirigami that I installed through Flatpak like Haruna, EasyEffects or the Clock app and they don’t follow my system icon theme. I am using latest Plasma version, but I had the same experience on Gnome too. I used these commands to give Flatpak access to my themes:
flatpak override --user --filesystem=xdg-data/themes:ro
flatpak override --user --filesystem=xdg-data/icons:ro
flatpak override --user --filesystem=xdg-config/gtk-3.0:ro
flatpak override --user --filesystem=~/.icons:ro
This does the job for GTK3 or even LibAdwaita apps, but Kirigami apps seem immune to this and keep on using Breeze icons.