I just applied Stefan's patch  to the march master of flashrom and
tested it on a Winyao WYI350T dual intel NIC:
04:00.0 Ethernet controller : Intel Corporation I350 Gigabit
Network Connection [8086:1521] (rev 01)
and successfully found a flash chip:
Found Micron/Numonyx/ST flash chip "M25P40" (512 kB, SPI) on nicintel_spi.
After dumping the firmware, writing a new iPXE rom everything seems to work:
Reading old flash chip contents... done.
Erasing and writing flash chip... Erase/write done.
Verifying flash... VERIFIED.
/tmp/bootutil64e -nic 1
1 2C534A012460 4:00.0 Gigabit YES PXE Enabled
Just gotta figure out how to append pxe and uefi images now :)