Simple issue of Production Serialization

As Jake said, the configuration memory used for AS (active serial) configuration of the FPGA is just a fairly standard SPI flash IC. In fact, it is even possible to use non Altera SPI flash for this purpose.

The FPGA will load it's configurtion starting from the begining of the flash. You can store whatever you want, including serial numbers, towards the end of the flash. Once the FPGA is configured, you can access the flash via the SPI interface.

The programming house does not necessarily even need to know that you are using an FGPA. Just give them the image for the SPI flash memory and tell them a location to program the serial number.