Using MIL-DTL-38999 circular connector for Ethernet applications
In many MIL applications, we are not looking for 100% compliance with an industry standard such as IEEE802.3.  Compliance is needed to ensure that a piece of equipment works with whatever it's going to be connected to - not some arbitrary piece of commercial gear.  Things we usually care about are physical and link layers of the OSI model, and maybe the network (IP) and transport (UDP/TCP) layers.

With '38999 connectors, you can achieve the desired DC voltage isolation requirement of IEEE802.3, if that's really needed, by 1) not using pins next to the connector shell and 2) removing pins around the Ethernet signals.