Jeremy,
I can confirm that SYNcookies are NOT part of the firewall mechanism of the 
kernel.

CONFIG_NETFILTER option in linux 2.6 is the toggle for linux packet
filtering support called 'netfilter'(iptables)... There are many sub-
choices/options for netfilter.

CONFIG_SYN_COOKIES however is a different choice, that allows you to
enable/disable compiling support for SYNcookies SYN-flood-defense
support.

Please also note that you generally cannot properly 'firewall out' a
typical spoofed-source SYN flood without preventing legitimate access to
your server.

-- 
proc/sys/net/ipv4/tcp_syncookies=1 should be seriously considered to permit SYN 
flood defense...
https://launchpad.net/bugs/57091

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