The down side is that while it does have the capabiilty to run its own prediction, I've not managed to get fully stable prediction yet.
On the up side, my csqc mod is able to predict teleporters, unlike any QW engines. It just goes a bit weird when you bunnyhop too fast. Bah.
But yeah, the engine checks the csqc so the weakest link is still that the engine source is available.