Other sources can override form factor filtering
When an app is available from multiple sources (in this case, apt and flatpak) and the newer version of them is not marked as adaptive, the app fails the adaptiveness check and isn't displayed in PureOS Store at all.
This happens for instance with GNOME Chess and Lightsoff - their deb versions are marked as adaptive, but flathub ones aren't. This results in them disappearing from the list when flathub repo is configured.