Didn't think it will be that quick, but here are two another quirks with TE0722:
1. I've removed Xmod and applied an external supply to 3.3V pin (from Keithley source), but TE0722 does not boot up - red LED light is lit. However it boots up ok when on external supply, Xmod mounted and its mode set to external 3.3V (SW1 ON, SW2..4 OFF). Does TE0722 require a specific set of values on JTAG or UART pins from J2 connector on power-on to boot? I suppose Xmod doesn't apply any sequence on power-on there, and I don't see any other reason for Zynq to not start.
2. I've tried to short RESn pin (called NRST on schematic; applied to POR-circuit that feeds POR_B signal) to ground to issue a hardware reset without removing the supply, and Zynq doesn't seem to reboot in any configuration (Xmod powered or ext. supply). It either doesn't boot at all (red LED light lit) or doesn't work after boot (UART inaccessible). (update: I've checked it again, POR_B is working with Xmod applied, Zynq resets correctly; probably it was the issue with parasitic capacitance which didn't release the NRST signal)
These two questions are rather important as we are designing a carrier board now.