i have two ALIX.2D13, both in a case, both already using all 3 ports.
for sync its recommended to use a separate interface.
i am wondering now if there are any minipci ethernet adapter available. that way i could connect the two boards neatly inside the box.
i searched a bit but only found wlan or minipcie.
Cards like that are available though they have mostly been replaced by pci-e cards as you found. Fortunately the world of industrial embedded PCs often moves at a glacial pace so that there are many, many boards with minipci slots still in the field. For example:
They're not cheap though!
Something cheaper on Ebay. No idea what chipset they are and listed as 'untested' though. ::)
Or this one from the same seller which is listed as new as is a Commell MP-541, an Intel 82541PI chipset which should work:
Twice the NICs for only $2 more!
Obviously never tried it myself though. ;)