Does Secure Email Threat Defense honor senders or domains from an allow list in Microsoft 365?

Yes, for businesses using journalled traffic sources. Secure Email Threat Defense honors senders and domains added to your spam filter allow lists in Microsoft 365 for Spam and Graymail messages. MS Allow lists are not honored for Threat verdicts (BEC, Scam, Malicious, Phishing); these items will be remediated according to your policy settings.

In the Microsoft Defender, you can access this setting here: https://security.microsoft.com/antispam

Microsoft Allow lists are not always honored by Secure Email Threat Defense if your organization allows individual users to configure allow lists in their mailbox and a message happens to fall in a user’s allow list. If you want Secure Email Threat Defense to honor these settings, deselect the Apply policy to Microsoft Safe Sender messages check box on the Configuration > Global settings > Unwanted message analysis panel. Safe Sender flags are respected for Spam and Graymail verdicts, but are not respected for Threat verdicts. That is, Safe Sender messages with Spam or Graymail verdicts will not be remediated.