When auto-publishing rules for Intune Applications are created, Patch My PC will create the Win32 application in Intune, however it will not automatically assign the application.
As mentioned in the comment of idea PATCHMYPC-I-1835, I understand that this is by design because there is a concern for hitting the policy size limits in Intune. The Dynamic Assignments feature used to publish Intune Updates automatically provides customers a mechanism to keep Intune policy size under control quite well. However, some business processes require the need for Intune Applications also to be dynamically assigned to certain groups.
If Intune Applications had the same Dynamic Assignment capability, then they could leverage this same control to keep policy size down while automatically publishing new applications dynamically to groups based on the defined criteria.
I believe having this feature for both Intune Applications and Intune updates would allow customers the flexibility they need to conform to their business requirements.
Thank you for your time.