IP is fairly high in the TCP/IP layer stack[1], isn't it? So it shouldn't be too surprising that a transport layer (or link layer? Not quite sure) does not use it, should it? 1. https://en.wikipedia.org/wiki/Internet_protocol_suite
What the satellites have to deal with is pysical/link level protocol to send packets from one to another (and from and to ground stations) as well as a network level protocol to route traffic inside the SpaceX network.