It might improve email situations if Koha had an option for all outgoing notices to go through a single email address, rather than the individual libraries. This would make it easier for patrons to whitelist a single address, rather than multiple addresses if you are part of a consortium. Emails could also be set with a reply-to address, that could be redirected back to the library that would have originally sent the email, which at that point would make it clearer to email systems that a conversation is being had between the two addresses. In theory. I could be totally wrong about all of this, but in my simple mind, this seems like a better work flow for notices. Although, maybe sending everything out through one address might raise flags quicker? I don't know.
Set the branch reply-to to the library email address and the branchemail to the same address for every library. That should achieve what you describe.