I guess it depends on what you are trying to achieve.

If you have physical desktops and virtual desktops and only want to package applications once I could see a good reason to go for SCCM when installing applications.

Only thing is that you need to make sure to SCCM agent doesn't "bloat" your appstack with unnesesarry information. I would check to see if there are files from the agent included in the appstack and if so make sure to filter them out.

On the other hand. SCCM uses an MSI to distribute applications. You could just as good get the MSI and install it manually just like you would install it with SCCM, then you still have the benefit of SCCM and only "packaging" once but not the downside of the bloatware and management of it in an appstack.