Did you find a fix for this? I have the exact same problem. I have two POP3 accounts. On my S6, the "When deleted from Inbox" option worked great. If Outlook is not open on my PC, emails come to my phone. When I get home and open Outlook, which is set to remove emails from the server after downloading, then the next time my S6 checked for emails, the ones that were pulled into Outlook automatically disappeared from my phone. My brand new S7 has the same option for POP3, but it does NOT work. I get dozens of emails a day. There's no way I want to manually delete. I need this fixed.
UPDATE: after playing around, I figured this out. Even though my mail accounts are POP accounts, I sent them up on my Galaxy S7 as IMAP accounts. That way, once Outlook on my PC (using POP) pulls the email down, it automatically disappears from my phone. Perfect for me as I only want to see my email on my phone when I'm out of the office. Once I pull it into Outlook, I want it gone off my phone.