It seems that EOP changed the option for turning off the Junk Email folder from the Anti-Spam threat policy. Even if your policy defines that you do not want spam going to the junk email folder, their new algorithm will still send it there. In my setup we prepend messages with text in the subject that might be spam and quarantine messages considered to be high confidence as spam. The possible spam messages have always been sent to the inbox so the user can review.
Looking for suggestions on how to bypass this in order to have a spam policy, but prevent it from going to the junk email folder where legitimate emails can be missed by the end users.
See here for more information on the change:
"EOP now uses its own mail flow delivery agent to route messages to the Junk Email folder instead of using the junk email rule. The Enabled parameter on the Set-MailboxJunkEmailConfiguration cmdlet no longer has any effect on mail flow. EOP routes messages based on the actions set in anti-spam policies. The user's Safe Sender list and Blocked Senders list will continue to work as usual."