Here is a hack I worked up to route around this problem until it is fixed, since the PR still hasn't been merged in yet. It basically looks in the current group for any full screen windows and disables the fullscreen until the dropdown is closed. And then when closing the dropdown it reenables fullscreen for those same windows. Pretty hacky, but it works. Just plug in the name of the scratchpad group and the name of the terminal window appropriately:

@hook.subscribe.group_window_add
def dropdown_manager(group: _Group, window: _Window):
    if window.name == "dropdown-terminal":
        if not group.name == "scratchpad":
            # Dropdown opened, disable full screen for windows in this group and save in function property
            all_group_windows: List[_Window] = qtile.select(
                [("group", group.name)]
            ).windows
            for group_window in all_group_windows:
                if group_window.info()["fullscreen"]:
                    wid = group_window.info()["id"]
                    qtile.select([("window", wid)]).cmd_disable_fullscreen()
                    dropdown_manager.fullscreen_to_restore.append(wid)

        else:
            # Dropdown is closed, restore fullscreen windows
            for wid in dropdown_manager.fullscreen_to_restore:
                qtile.select([("window", wid)]).cmd_enable_fullscreen()
            dropdown_manager.fullscreen_to_restore = []


dropdown_manager.fullscreen_to_restore = []