You've got confused - that section is referring to options to automake itself.
It's a way of setting the automake command-line options:
-W CATEGORY
--warnings=category
Output warnings falling in category. category can be one of:
gnu
warnings related to the GNU Coding Standards (see Top).
obsolete
obsolete features or constructions
override
user redefinitions of Automake rules or variables
portability
portability issues (e.g., use of make features that are known to be not portable)
syntax
weird syntax, unused variables, typos
unsupported
unsupported or incomplete features
all
all the warnings
none
turn off all the warnings
error
treat warnings as errors
A category can be turned off by prefixing its name with ‘no-’.
For instance, -Wno-syntax will hide the
warnings about unused variables.
The categories output by default are ‘syntax’ and ‘unsupported’.
Additionally, ‘gnu’ and ‘portability’
are enabled in --gnu and --gnits
strictness.
The environment variable WARNINGS can contain a comma separated list of
categories to enable. It will be taken
into account before the command-line
switches, this way -Wnone will also
ignore any warning category enabled by
WARNINGS. This variable is also used
by other tools like autoconf; unknown
categories are ignored for this
reason.
The per-file listed in section 17 refers to per-Makefile not source file.
I'm not aware of any per-source file flag setting, but you can set the option for each result binary with:
binaryname_CXXFLAGS