In the XPS / PlanAhead flow a Zynq MIO Configuration change of IO Standard does not have effect in the PlanAhead tool.
For example, if I create an XPS Zynq design, then run implementation in PlanAhead and check Pad Report, I can see that the IO Standard is as I set it, LVCMOS33.
However, if I want to change to LVCMOS25, I re-open the XPS design and change the MIO IO Standard setting in the Zynq PS MIO Configurations, then close XPS, and rerun synthesis and implementation in the PlanAhead tool.
When I check the Pad Report in PlanAhead, I see that the IO Standard is not changed and it can be seen in the new "system_stub.ucf" that this was not updated with the new setting of LVCMOS25, even though this ucf is regenerated.
To work around this issue, clean the netlist using the Hardware -> Clean Netlist in XPS.
Close XPS and re-run synthesis and implementation in the PlanAhead tool.