The purpose of these connections are for additional feature options that can be added at time of ordering. extra NIC ports, Thunderbolt, graphics cards, extra hard disks etc
Reference to service manual as following, anyone know the purpose of connector on system board? [URL] E?? connector (1,4,19,20) P30 connector (22) Optional 2.5 GbE RJ-45 connector (2) Thunderbolt 4 AIC connector (18) CAC_PIV power connector (21) Hard drive fan connectors (24) why one of two no socket and there are not PWN 4 pin socket? Optional video card connector (34) USB-C connector (35)  
What is the purpose of the Precision 3650 system board connector?