The latter is not officially "wrong", but *is* terribly anachronistic.
I think automake documentation or comments call that syntax obsolescent.
* cfg.mk (_makefile_at_at_check_exceptions): Exempt @SCHEMADIR@
and @SYSCONFDIR@ uses -- there are no Makefile variables for those.
* docs/Makefile.am: Use $(INSTALL), not @install@.
* examples/dominfo/Makefile.am: Similar.
* examples/domsuspend/Makefile.am: Similar.
* proxy/Makefile.am: Similar.
* python/Makefile.am: Similar.
* python/tests/Makefile.am: Similar.
* src/Makefile.am: Similar.
* tests/Makefile.am: Similar.