iMPACT supports only 64kB sector size. From the Spansion website, the only 512 Mb Spansion device (S25FL512S) is 256kB sector size. iMPACT only supports 64kB sectors for 128Mb and 256Mb devices, but for 512Mb the only part Xilinx supports are 256kB sectors.
Sector size is really only a factor for erase. These parts, as well as most of all SPI flash devices will read at a byte level and program (write) on a page level or even on a byte level. So, it is certainly possible to read and program the 4kB (byte) sectors. However, this is beyond the scope of iMPACT. iMPACT will only erase on the 64kB sectors and will program using the page programming command. More granularity than 64kB erases is rarely a need for FPGA configuration because there are not many bitstreams that are smaller than 64 kB.