Active serial configuration flash (EPCS & EPCQ) vs normal SPI flash
Each EPCS device has a so called "silicon ID" which can be used to identify its type, which can then be used to look up the size of the flash memory. Quartus II can read this value and then check e.g. if the device is large enough for the generated bitstream.  

There is a neat documentation about structure and operation of Altera EPCS devices, to be found on the Altera homepage. You can think of EPCS devices as a special type of SPI flash with a few special features for storing bitsreams used to program your FPGA. It's just a little less fuzz to use an EPCS than a standard SPI flash with your Altera FPGA.