minor regression: config header templates

When testing the latest automake with autoconf-2.69, all of automake's
tests pass. But with the latest autoconf (built from master) in my
path, two tests "FAIL", as below. I bisected to v2.69-181-g78ad1b0b,
aka https://git.savannah.gnu.org/cgit/autoconf.git/commit/?id=v2.69-181-g78ad1b0b

I plan to release automake-1.16.2 very soon (from master), maybe even
tomorrow. This does not block my planned automake release, but it'd be
great to resolve soon, nonetheless.

FAIL: t/autohdr4
================

Running from installcheck: no
Test Protocol: none
PATH = /home/j/w/co/automake/bin:/home/j/w/co/automake/t/ax:/usr/share/Modul
es/bin:/usr/lib64/ccache:/home/j/bin:/p/bin:/usr/local/bin:/sbin:/usr/sbin:/
bin:/usr/bin:/usr/games:/usr/local:/usr/local/bin
++ pwd
/home/j/w/co/automake/t/autohdr4.dir
+ cat
+ mkdir sub1 sub2 sub3
+ :
+ echo '#define NAME "grepme1"'
+ cat
+ cat
+ cat
+ aclocal-1.16 -Werror
+ autoconf
+ autoheader
autoheader: cannot open sub2/config.${BOT}: No such file or directory
+ am_exit_trap 1
+ exit_status=1
+ set +e
+ cd /home/j/w/co/automake
+ test none = tap
+ case $am_explicit_skips in
+ test 1 -eq 0
+ keep_testdirs=yes
+ am_keeping_testdirs
+ case $keep_testdirs in
+ return 0
+ set +x
FAIL t/autohdr4.sh (exit status: 1)

FAIL: t/autohdr-subdir-pr12495
==============================
... similar.

Full disclosure, bisection details:

# Build at each iteration with this:
autoreconf -vi && ./configure --prefix=/tmp/ac && make && (
PATH=`pwd`/tests:$PATH; autoreconf -vi ) && make install

# Test like this:
(cd ~/automake && PATH=/tmp/ac/bin:$PATH make check TESTS=t/autohdr4.sh)