Note: while the use-case described is about using submodules within a project, the same applies to a normal git clone of a repository over HTTP.
git clone
I have
If you just want to use proxy on a specified repository, don't need on other repositories. The preferable way is the -c, --config option when you git clone a repository. e.g.
-c, --config
$ git clone https://chromium.googlesource.com/chromium/tools/depot_tools.git --config "http.proxy=proxyHost:proxyPort"