if I switch my main application to use Autoconf or Libtool, then I can bundle GPL code under proprietary terms?
No, unless in the very unlikely case that the specific GPL code in question grants you that right as its own special exception. Only someone who controls the rights to a given project can offer you license terms for that project, no matter what technologies are involved. A third party cannot grant you an exception.
What you are looking at are special terms in the licenses of various scripts from the Autotools that are copied (usually by the Autotools themselves) into the project source tree, with the intent that they be distributed with the project. This copying and redistribution serves the Autotools' design goal of providing for independent software distributions. That is, you don't, in principle, need to have the Autotools themselves installed to build a project that has an Autotools-based build system.
Although these scripts are part of the Autotools, the Autotools maintainers do not want to limit the Autotools' use to GPL-licensed projects. Each license exception is therefore granted to allow the script in which it appears to be distributed as part of an autotools-based build system for any project (the "it" refers to "this file"). That also explains why the various exceptions carry a limitation to projects with an Autotools-based configure script or that are built with libtool, and why it specifies that the scripts may be distributed under the same terms as the rest of the project: the exceptions are tailored to be as narrow as possible while serving their purpose.
There is a related issue revolving around the
configure script generated by autoconf and the
Makefile.in templates generated by automake. These generated files contain significant pieces of code that belong to the respective tools, and they are intended to be distributed with the project. I take these to be what @amon means by "the build scripts generated by autoconf", but these are not the files to which the license exceptions in question apply. Instead, each of these files bears its own, much more permissive license grant. For example, from a configure script generated by autoconf 2.69:
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
# This configure script is free software; the Free Software Foundation
# gives unlimited permission to copy, distribute and modify it.
More generally, although it is not an absolute rule, the FSF is pretty consistent about putting copyright statements and statements of rights directly in the files to which they apply, and it is their recommendation that others do the same.