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[<woodq11 AT gmail.com>]

Yes. The reason I use iptables when I'm using Tor is to avoid needing software
that supports fully running traffic through a SOCKS proxy. This is called
transparent proxying, and in my case doesn't yield any negative side-effects
(unless you could not being able to use torrents, which isn't a big deal for
me given that doing so would be rude to Tor network operators and users.)