It appears that gjs is responsible for wrapping arrays in unnecessary variants in DBus results. This happens for ObserverChannelFilter property of the GNOME Shell Telepathy Client that implements the Observer interface.

The ObserverChannelsFilter is defined in gnome-shell/js/ui/telepathyClient.js as

    get ObserverChannelFilter() {
        return [ singleUserTextChannel, oneOrMoreUserTextChannel ];
    },

where, e.g.
let singleUserTextChannel = {};
singleUserTextChannel[Telepathy.CHANNEL_NAME + '.ChannelType'] = Telepathy.CHANNEL_TEXT_NAME;
singleUserTextChannel[Telepathy.CHANNEL_NAME + '.TargetHandleType'] = Telepathy.HandleType.CONTACT;

The signature for the method is defined in gnome-shell/js/misc/telepathy.js as

    properties: [
        { name: 'ObserverChannelFilter',
          signature: 'aa{sv}',
          access: 'read' }
    ]

The output of dbus-monitor shows that the extra variants get added into the result:

method call sender=:1.126 -> dest=org.freedesktop.Telepathy.Client.GnomeShell serial=577 path=/org/freedesktop/Telepathy/Client/GnomeShell; interface=org.freedesktop.DBus.Properties; member=GetAll
   string "org.freedesktop.Telepathy.Client.Observer"
method return sender=:1.165 -> dest=:1.126 reply_serial=577
   array [
      dict entry(
         string "ObserverChannelFilter"
         variant             array [
               variant                   array [
                     dict entry(
                        string "org.freedesktop.Telepathy.Channel.TargetHandleType"
                        variant                            int32 1
                     )
                     dict entry(
                        string "org.freedesktop.Telepathy.Channel.ChannelType"
                        variant                            string "org.freedesktop.Telepathy.Channel.Type.Text"
                     )
                  ]
               variant                   array [
                     dict entry(
                        string "org.freedesktop.Telepathy.Channel.TargetHandleType"
                        variant                            int32 0
                     )
                     dict entry(
                        string "org.freedesktop.Telepathy.Channel.ChannelType"
                        variant                            string "org.freedesktop.Telepathy.Channel.Type.Text"
                     )
                  ]
            ]
      )
   ]

Compare this to the format of a similar filter specification from Empathy:

method return sender=:1.168 -> dest=:1.126 reply_serial=597
   array [
      dict entry(
         string "HandlerChannelFilter"
         variant             array [
               array [
                  dict entry(
                     string "org.freedesktop.Telepathy.Channel.TargetHandleType"
                     variant                         int32 0
                  )
                  dict entry(
                     string "org.freedesktop.Telepathy.Channel.ChannelType"
                     variant                         string "org.freedesktop.Telepathy.Channel.Type.Text"
                  )
               ]
               array [
                  dict entry(
                     string "org.freedesktop.Telepathy.Channel.TargetHandleType"
                     variant                         int32 1
                  )
                  dict entry(
                     string "org.freedesktop.Telepathy.Channel.ChannelType"
                     variant                         string "org.freedesktop.Telepathy.Channel.Type.Text"
                  )
               ]
               ...
            ]
      )
   ]

The way we were specifying the filter did not cause any problems on F12, but it fails on F13 causing us not to get any message notifications, with 'MC_DEBUG=1 /usr/libexec/mission-control-5' indicating:

(process:24923): mcd-DEBUG: _mcd_client_proxy_observer_get_all_cb: org.freedesktop.Telepathy.Client.GnomeShell ObserverChannelFilter absent or wrong type, assuming no channels can match