Flatpak is not a container and should not be thought of as such for security/privacy purposes:
In general though we try to avoid using the term container when speaking about Flatpak as it tends to cause comparisons with Docker and rkt, comparisons which quickly stop making technical sense due to the very different problem spaces these technologies try to address. And thus we prefer using the term sandboxing.
https://flatpak.org/faq/#Is_Flatpak_a_container_technology_
It can provide container-like functions if specifically configured for that, but that's not normal and it shouldn't be relied on as a security barrier.