Yes, they do not currently support the 2 GBit flash device. It is also not supported in Quartus 15. They did however add it to the wish list, so i guess it will come in future.
For now we modified U-boot, and use U-Boot as a intermediate step between SPL and our Bare Metal application to load the FPGA, and application, and it also provides functionality to Flash the 2 Gbit device.
So in production we need a DS5 with license to load Uboot initially to flash the device. Thereafter we can used text terminal with Y Modem to flash the device.
As soon as Altera bring out the support for the device, i will change the production programming process with cygwin cmd prompt programming options of Altera.
Hope it helps.