The Autoptimize works perfect without using CDN.
As soon as CDN is used, Autoptimize stops working.
Thats to bad as CDN is vital for some websites.
I use the CDN Linker from GitHub.com to connect with my account with SoftLayer. So far the only plugin that works with CDN is the JS & CSS Script Optimizer Plugin (The JS works - but not the CSS).
So it seams to be hard to find a plugin that optimizes both JS & CSS and have it both working with CDN.
Hopefully Autoptimize can solve this and make it a highly desired plugin.
Cheers RK