I want to Share my current experience as this issue was esacalated at higher level.(some application that will generate email needs to go live)
We have implemented Safe Sender list via GPO & from outlook we can see that its getting in there.
But it is not working as expected, emails from the domain in safe sender list was still going to Junk folder.
We have logged a case with MS but with no success as they were suspecting the email junk rule corruption & want us to use mfcmapi to remove
Junk email rule message from the mailbox as they have seen this with other customer but our case turned out to be different.
I have started troubleshooting , found that OWA list & Outlook safe sender list are not in sync for many users.
Then I have coordinated with our AD team to check the GPO if evrything is perfect & the answer was yes, eventually I have opened the safesender list & found that there are spaces at the tail, so I have asked the AD team to remove those.
After doing the above issue got resolved.