Using New Outlook on Windows for personal email, calendar, and contact management
I think I was able to find a fix for this. If you go to the "View tab" and then "View settings", then "Compose and reply" and then check off "always show bcc" and "always show From", it seems to properly reply from the shared email (and not from the main account email). It doesn't fix the viewing settings -- my shared inboxes are still (frustratingly) buried but at least I don't have to panic about where the emails are being sent from.