You are supposed to cd to the subproject and run autoconf/automake etc.
there, i.e. the steps you don't want to do are the nominal procedure.
Some projects try to automate this by using a manually written script,
in most cases called autogen.sh or bootstrap.
In case all of your configure scripts and Makefiles are compatible to
using the same versions of autoconf/automake etc. you alternatively can
try to use "autoreconf" in the toplevel directory.
But beware, autoreconf can be dangerous and doesn't always work.
Ralf