UG933 contains the following information:
"Byte and bit swapping is allowed to facilitate PCB routing, except for LPDDR2, which specifically forbids swapping. When swapping bits, keep all bits within the same byte group."
What this means is that pin numbers can be swapped between Zynq and the SDRAM within a byte, or entire byte groups can be switched.
Since these pins are fixed
on Zynq there is nothing you can do to swap these within Zynq or Vivado.
Instead, you would need to physically route different numbered pins together
For example, this could be done in cases where routing is much easier if DDR3 pins DQ and DQ could be switched.
Since this is allowed, it is possible to route pin DQ from Zynq to DQ of the memory and vice versa.
Since data will be returned the same way it was sent out of the Zynq PHY interface, physically swapping data lines between Zynq and memory will have no net effect on the data.