Step one - copy system lynx.cfg:
cp /etc/lynx.cfg ~/
Step two - modify your ~/lynx.cfg to your heart's content.
Step three - launch lynx with your custom cfg:
lynx -cfg=~/lynx.cfg <url>
It's possible older versions of lynx did not allow you to specify a config, but you can with my version.
Lynx Version 2.8.6rel.5 (09 May 2007)
libwww-FM 2.14, SSL-MM 1.4.1, OpenSSL 1.0.0-fips, ncurses 5.7.20090207(wide)
Built on linux-gnu Nov 23 2010 12:44:01
Copyrights held by the University of Kansas, CERN, and other contributors.
Distributed under the GNU General Public License.
See http://lynx.isc.org/ and the online help for more information.
See http://www.openssl.org/ for information about OpenSSL.