With VX.2.2 or later the I/O optimizer tool, there is no difference in terms of pin swapping. See the "Allow swap and unravel between partitions" pin partition property for more details. Signal assignments to pins can be swapped within or between partitions when this property is set to "True".
The advantage of creating a customized FPGA component using the FPGA Wizard from the design entry tool is that you will be able to modify and add pin partitions. By tailoring the pin partitions to reflect the I/O interface of the FPGA project can make the optimization task easier and produce better results.
Hope this helps!