I know you mentioned they use the same runtime, but I have noticed some difference in performance, for the better too. In fact, I had old instances of games that I couldn't add effects to simply because it would cause fps drops, but now have been able to add the effects I previously wanted to and see much better performance overall.
It could be the new compiler or perhaps just Android optimizations, but it runs as smoothly as iOS now (which ran great on C2 and now C3). Either way, I have noticed increased performance since using C3 regarding Android usage.
-For the record, I am talking about Intel XDK performance vs the built in compiler for Android in C3