the Zend Engine (the Zend directory in the php-src) had until many
versions ago option for a standalone built without PHP extensions,
TSRM and other PHP core parts.
Once this was possible:
cp -r /path/to/php-src/Zend /path/to/zend-engine
./buildconf && ./configure && make && make install
Automake was once part *nix (Linux, macOS...) build system and was
later removed from the PHP part.
However, today there still exist some files specific to the standalone
built of Zend Engine which require Automake and would need some
refactoring and refreshments. Maybe even some C code patches to be
able to build a fully standalone Zend engine without other php-src
There is a pull request opened  to remove the standalone built of
Zend Engine because these files no longer work and they include some
obsolete Autoconf macros. To not confuse the end PHP user how to
properly build php from source, I think it's best to remove them from
tracking in the Git repository. If there is such a case where separate
built would be required, a separate project specific files might be a
better pick. Either using Autotools (like PHP does) or something else
such as CMake.
If there are any objections in this regard, let me know please so we
don't remove maybe something important from the contextual
understanding of the PHP build system itself.