I understand the problem now.  You have an aclocal.m4 that defines GTK_DOC_CHECK, so the m4_ifdef evaluates true and autoreconf does observe a use of the macro and therefore tries to invoke gtkdocize.

In order to figure out how to make autoreconf reliable regardless of what's available on the system, we're going to need to read up on actual uses of gtk-doc and also on what pieces of it people tend to have installed, and there isn't time for that before the next release, so I'm marking this deferred.

I tried just now to flesh out the fragment you provided into a complete test case, and I failed.  Given this configure.ac

AC_INIT([issue110503], [1])
AM_INIT_AUTOMAKE([foreign])

# check for gtk-doc
m4_ifdef([GTK_DOC_CHECK], [
GTK_DOC_CHECK([1.14],[--flavour no-tmpl])
],[
AM_CONDITIONAL([ENABLE_GTK_DOC], false)
])

AC_CONFIG_FILES([Makefile])
AC_OUTPUT

and a stub Makefile.am to match, autoreconf -iv prints:

autoreconf: export WARNINGS=
autoreconf: Entering directory '.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal
autoreconf: configure.ac: tracing
autoreconf: configure.ac: not using Libtool
autoreconf: configure.ac: not using Intltool
autoreconf: configure.ac: not using Gtkdoc
autoreconf: running: /usr/bin/autoconf
autoreconf: configure.ac: not using Autoheader
autoreconf: running: automake --add-missing --copy --no-force
configure.ac:2: installing './install-sh'
configure.ac:2: installing './missing'
autoreconf: Leaving directory '.'

This with Autoconf 2.71.  Please supply us with a complete configure.ac that reproduces the problem.

I'm not sure what happened to the documentation but to see what it looks like, here is the archive version of it:

https://web.archive.org/web/20210306043255/https://developer.gnome.org/gtk-doc-manual/stable/settingup_autoconf.html.en

This worked fine with previous versions of autoconf, as side-effect of the new feature this is now broken. Even if this only ever worked by luck, clearly projects out there relied on this method to achieve something that seems quite useful behavior: Keep gtkdocize optional for people who do not care about generation of the documentation.

Two projects that use the problematic snippet are gnutls and harfbuzz.

Can you clarify what you mean by self-contained example? All it takes is to create a configure.ac with the snippet I quoted in the previous comment and run
autoreconf -fiv.

A possible workaround for other people stumbling over this bug report is to set gtkdocize via an env variable to a different "dummy" tool:

GTKDOCIZE=false autoreconf -fiv

Even if this is now what it is and can not be fixed or there is no desire to, it would be quite helpful for autoreconf to fail with a more descriptive error than:

> Can't exec "gtkdocize": No such file or directory at /usr/share/autoconf/Autom4te/FileUtils.pm line 293.
> autoreconf: error: gtkdocize failed with exit status: 2

Something like:

> gtkdocize is required by this project but could not be found

Looks like I can't change the title, this is of course not a regression but a side-effect of the new feature. (I wrote the title before doing the full investigation where this error came from and forgot to change it)