With the first few points, I feel like these are probably things that will either get easier as you adjust to the Gnome workflow, or can be remedied by extensions. I recommend installing the unofficial Extension Manager app my Matt Jakemen, which comes with a built-in search. Makes finding extensions very convenient.
The issues with the notifications sounds a bit weird. They shouldn’t be taking focus away from the app you’re working on. I use Thunderbird all the time and it never does that to me. Also, xfce-notifyd? What is that running on Gnome?