PI and ST:R were developed completely independently. I didn't even know PI had anything to do with ST until I played it. And there are a lot of fundamental conflicts - two Hadeses instead of one, a completely different ship armament, different campaign back stories, etc. They're not at all compatible. Consider them as taking place in alternate universes.
Now, on the other hand, ST:R is compatible with Blaise Russel's universe. There's a fairly obvious crossover with Shrouding the Light, and there's a not-so-obvious crossover with Echo Gate that we arranged while he was developing it. There are also other, smaller, touches that some people might notice.