I did see a post for it here, but it was quite old.
I noticed that "Ad Injection" had no issues with WP Super Cache, it just needs it to be placed in legacy mode and uses its 'mfunc tags'. So it must be possible with AdRotate.
Has that been updated at all? It's been a year and a major WP version since it was last asked. I would simply use Ad Injection, but it doesn't let me track clicks on our custom ads.