At my current customer, we are currently switching over to SCCM for all Software Update Management.
For now, the only issue we are experiencing is that we do not receive SharePoint updates on our SharePoint Server 2013 farm. With WSUS we can detect these, but they are not listed in SCCM. We sync directly with Windows Update.
It are specifically the updates that are marked as "farm-deployment", as you can see in example in this image.:
http://2.bp.blogspot.com/-gI8Ew7RlY0g/VPqM0QUn6oI/AAAAAAAAIDQ/S1Ufp0x-mSU/s1600/windows%2Bupdate%2Bincludes%2Bsharepoint%2B2013%2Bpatches.png
In the SUP properties, we have enabled the Office 2013 product and all classifications besides "Tools".
Am I missing something?