Terminal resistor function on JTAG SMT2 schematic
I think they are to let the external JTAG programmer remain connected without disrupting the JTAG line between the SMT2 and Zynq. The SMT2 can overpower the external JTAG with the resistors there.

Unsure how the SMT2 doesn't always overpower the external programmer though. I would have put resistors to allow the external programmer to overpower the SMT2 because you can unplug the external programmer and make it go away.