Hi Jan & Anantha,
Thank you for posting comments.
Once the workloads is switched to Intune, Intune will have the capability to deploy apps, and at the same time for SCCM, the capabilities is not removed.
After you transition this workload, any available apps deployed from Intune are available in the Company Portal. Apps that you deploy from Configuration Manager are available in Software Center.
I just finished testing deploying .msi app installer as available type from SCCM to co-management devices after client app workload switched to Intune. The app will still appear in Software center and can be installed without any issue.