Enable flatpak tests that require libmodulemd
    
    These tests were skipped previously.
    A virtual environment in Jenkins tests needs access to site packages.
    Currently, the latest libmodulemd package is installed for Python 3.9
    and therefore the tests for flatpak can run only in this environment.
    Other minor changes are for synchronization of environment versions
    with Jenkins dockerfile.
    
    Signed-off-by: Ondrej Nosek <onosek@redhat.com>