I noticed, that Arria II GX isn't yet supported by an Altium library. But you should study how the existing FPGA libraries support pin swapping. There must be a detailed definition of swappable pins respectively pin pairs. In a real design, the choice of swappable pins depends on many details, e.g. selected bank voltage and I/O standard. Also the constraints set by the usage of other pins, and e.g. pin distance rules must be considered. It's not clear to me how it's achieved with one general library in Altium designer.
When I used pin swapping with other layout tools, I defined a specialized library based on the respective design enviroment. But I have only basic knowledge of Altium, I didn't use it yet for designs with FPGA.