The main problem I have with the PCEngines APU is that it has Realtek 8111/8169 NICs, while the Soekris net6501 has e1000 Intels... Realtek NICs tend, from my experience, to behave erratically under high load on Linux, and sometimes simply not work on FreeBSD and OpenBSD
The full-sized PCIe slot is also a nice touch.
(disclaimer: possible bias, am running a OpenBSD/net6501 as an edge router for a hackerspace)