At this moment, Atlassian supports the following MDM policies: 

• MDM security controls and supported apps

However, there isn't a method to configure the Atlassian Apps to be considered as managed apps on Intune.

For example, when trying to configure MAM policies via App Protection Policies, that results in the policy settings being ignored.  

This happens even after setting the app Bundle IDs and making the apps included in the list of custom apps. 

The reason behind this behavior is that Atlassian doesn't have a specific app version that was developed using Microsoft libraries.

Suggestion: 

Provide an Intune specific version for Atlassian mobile apps.

Workaround:

Currently, there is no workaround. It's possible to configure some MDM policies using AppConfig, Mobile Device Management Settings (iOS), and Android Enterprise (Android):

• MDM security controls and supported apps

It is also possible to configure MAM policies from the Atlassian Organization side:

• Security settings in a mobile app policy