Once you scan the code you stay logged in as long as the page is open on your phone, you can upload files as many times you want, not only once. But you cannot reuse the same link on other devices or browsers.
Yes I'm planning to add such settings.
Hmm this is an interesting idea, in my current implementation you need to re-pair your phone everytime you restart joplin, the pairing info is not persisted. Clients are also kicked out if they are inactive for quite some time. I think fixing these will reduce the amt of pairing one need to do significantly. I'm not very sure about PWAs or bookmarking links since the plugin uses local ips to communicate and they keep changing every time you change the network or even after every few days, depends on your router.