When I right click and hit Bookmark this Tree I get a notification saying Failed to get permissions to create bookmarks. Please click here to grant extra permissions. but clicking on it does nothing.
TST should request these permissions when installing so the experience is seamless when bookmarking a tree of tabs
Fails to prompt for permission
I've setup an ArchLinux environment (with Xfce4) and tried the operation. I think I've understood what you meant.
This is a screenshot what I saw.

When I click the notification itself, it becomes just closed and nothing happen. When I click the "Activate" button, TST opens the options page to grant the permission as I expected.
This looks to be a bug of Firefox itself. TST registers a listener for notifications.onClicked (notifications.onButtonClicked is not supported on Firefox) but actually the listener is called only when we click the "Activate" button in the notification.
On Windows the notification popup has no button and clicking on the notification itself opens the options page as I expected.
I use dunst for notifications and it doesn't support buttons so none are shown.

Why don't you request these permissions at install time instead of dynamically?
I found the option under Context Menu and enabled it. You can close this issue if you don't think you can enhance this UX.
Why don't you request these permissions at install time instead of dynamically?
There are some reasons:
manifest.json.permissions.request() is callable only from some limited cases due to security reasons. Sadly the event handler for the context menu is out of allowed cases.I found the option under Context Menu and enabled it.
Yes, the notification should open the options page and scrolls to the section when it is clicked. And it works as expected for me on Windows and Ubuntu. Thus I thought that it is a problem of WebExtensions API provided by Firefox itself or the notification provider of the platform.
That's absolutely fair. Thanks for explaining it well!
I misunderstood the restriction, permissions.request() is callable from the context menu actually.
But there is another restriction. When I called permissions.request() the permission popup does not appear, if the context menu is opened on a background tab. The requester is unexpectedly bound to the context tab instead of the active tab, so the popup is shown when I activate the tab after the context menu is closed. Hmm...
1679925 - Permission requesting popup is unexpectedly bound to the context tab instead of the active tab when permissions.request() is called from the context menu on a background tab
https://bugzilla.mozilla.org/show_bug.cgi?id=1679925
When I click the notification itself, it becomes just closed and nothing happen. When I click the "Activate" button, TST opens the options page to grant the permission as I expected.
The "Activate" button is defined here:
https://searchfox.org/mozilla-central/rev/168c45a7acc44e9904cfd4eebcb9eb080e05699c/toolkit/system/gnome/nsAlertsIconListener.cpp#181
Firefox's notification popup on Linux is implemented based on "libnotify". Sadly it looks to provide only an ability to handle an action bundled to a button, instead of a handler for clicking on the notification popup itself.
https://developer.gnome.org/libnotify/0.7/NotifyNotification.html#notify-notification-add-action
This looks to be a reason why clicking of the notification itself is ignored on my case.
On the other hand, dunst looks to override Firefox's notification with its own one. Dunst has ability to customize button actions via its config file, I think this looks to mean that Firefox's default button handler for the "Activate" button is ignored while dunst is running. If my understanding is correct, dunst is not compatoble to Firefox's full-featured notifications and it is a problem of dunst itself.
I've reported an issue to Dunst: https://github.com/dunst-project/dunst/issues/786
There are important information to use Dunst with Firefox: https://github.com/dunst-project/dunst/issues/786#issuecomment-736351219 and https://github.com/dunst-project/dunst/issues/786#issuecomment-736452341
dmenu (so you'll need to install it at first.)dunstctl action for the desktop environment.mouse_left_click = close_current in the ~/.config/dunst/dunstrc as mouse_left_click = do_action, close_current, then the notification will behave like the one on Windows and other platforms: clicking on the notification triggers the default action before it is closed.