In some programs like screen I couldn't figure out, how to correctly display line endings. With picocom it works. A bit too much new lines but the content is readable.

# picocom -b 115200 --imap crcrlf /dev/ttyUSB0

PC Engines: BIOS Update

With pfSense 2.3 and later pkg can be used to install software.according to the documentation it's not recommended

[2.3.2-RELEASE][root@pfSense]/root: /etc/rc.conf_mount_rw
[2.3.2-RELEASE][root@pfSense]/root: pkg install flashrom-0.9.9
[2.3.2-RELEASE][root@pfSense]/root: /etc/rc.conf_mount_ro

[2.3.2-RELEASE][root@pfSense]/root: flashrom -w apu2_160311.rom -p internal
flashrom v0.9.9-r1955 on FreeBSD 10.3-RELEASE-p5 (amd64)
flashrom is free software, get the source code at https://flashrom.org

Calibrating delay loop... OK.
coreboot table found at 0xdffae000.
Found chipset "AMD FCH".
Enabling flash write... OK.
Found Winbond flash chip "W25Q64.V" (8192 kB, SPI) mapped at physical address 0x00000000ff800000.
Reading old flash chip contents... done.
Erasing and writing flash chip... Erase/write done.
Verifying flash... VERIFIED.