gpg reads .gnupg/gpg.conf
Gpg used by enigmail will still read ~/.gnupg/gpg.conf.
Not sure if this is what you expect or if this could cause side effects with other (proxy) settings in (old) gpg.conf's.
This was discovered this accidentally, because I disabled throw-keyids in TorBirdy settings and still ended up with mails having this feature enabled, because in my ".gnupg/gpg.conf" the option "throw-keyids" was set.
I don't know if there is any --ignore-config command line option for gpg, if --homedir combined with --no-default-keyring is the only option to prevent this (which would have other side effects as well) or if this whole ticket is a non-issue.
In the latter case, sorry for the noise and feel free to close this ticket as invalid.