No dobut, LTE is an IP based technology. Information between different nodes of LTE are is exchanged by using the IP protocol.
But if you look each protocol stack of each interface then you will find every interface has different application protocol on top of IP layer.
S1- MME: This interface also uses underlying IP layer but on top of IP layer, SCTP (transport protocol) and S1-AP (Application Protocol is used). Similarly there are number of interfaces like S1-U (interface between SGW and eNodeB), S11 interface (MME to SGW) and so on interfaces uses different application layer to fulfill different requirements.
These are the few reasons having different path for control plane and data plane.
Please have a look into wireshark logs then you will come to know after IP address most of interfaces have different application layer protocols.