The JESD204 core version 4.0 (rev 1) for 2013.2 generated for Zynq does not include a watchdog for the GTX start up.
The watchdog timer is only generated for Virtex and Kintex devices.
The watchdog is not strictly required by the GTX.
However, this GTX watchdog timer logic in Zynq devices has been added in 2013.3, improving reliability for GTX startup in Zynq.
See (Xilinx Answer 58605) - 2013.3 Vivado IP Release Notes - All IP Change Log Information for more details.