MFT is good, as it configures it in the Firmware of the hca.
you could put the commands (echo .... ) into /etc/rc.local that would setup the mode at boot-time.
Flash the cards to MCX314A-BCBT (ethernet only) and you should be ok, they'll just be standard ethernet adapters, pretty sure most linux distros the drivers already. I can confirm Ubuntu does, so Debian probably does too.
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