mjsrc​ 

Thanks for the question, I appreciate the detail you provided. You're right that there's been a gap between the Security Compliance Toolkit baseline releases and what's available natively in Intune's Endpoint Security baselines. The Security Compliance Toolkit team released the M365 Apps v2512 baseline in December 2025 and work is underway to bring the Intune-native baselines in-line with that update. In the meantime, the Settings Catalog in Intune is updated way more frequently than the baselines and often has the individual settings you need. I'd recommend using them both: supplementing your baseline with Settings Catalog policies to cover any critical gaps.

You can also import the latest baseline GPO templates to make cross-referencing easier. Check out the baseline management guidance here: https://learn.microsoft.com/en-us/intune/device-security/security-baselines/configure-baselines.