Entirely possible that they do - you can't know for sure as it's proprietary software.

It's always been marketed as a rewrite from the ground up since Rome 1 - it definitely seems like it. I believe that Empire was another new engine...

I wouldn't hold your breath for a source release however. It's long been speculated that the code may not even be CA's or SEGA's to release. Both EA and Activision may be involved when it comes to Shogun/Medieval 1 source...