I've done some digging. According to the documentation, http://pcengines.ch/file/NCT5104D_Datasheet_V1_9.pdf, there are two revisions (or chip ID's) of the NCT5104D, a B (0xc452) and C (0x453) version. My APU2 seems to be the C revision chip.
The SP5100_TCO module in Debian 9 (kernel 4.9), does not have support for the above chip (rev. B and C).
The driver on PCEngine's github page does recognise the chip, but it is not a watchdog driver. https://github.com/pcengines/linux-gpio-nct5104d
[ 1825.718466] gpio-nct5104d: Found nct5104d at 0x2e chip id 0xc453
[ 1825.718582] gpio-nct5104d: platform_driver_register
[ 1825.719506] gpio-nct5104d: Device added
It seems that some are able to use /dev/watchdog if i2c_piix4 is unloaded, but on my board that won't help.
[ 87.275613] sp5100_tco: failed to find MMIO address, giving up.
In the mean time we could use the softdog workaround (software watchdog module) for detecting problems other than hardware / system lockups. Like network, filesystem, cpu load... Sysctl kernel.panic=<seconds> might come in handy also.
Thats all for now, have a nice weekend.