Sorry, that page is misleading when taken from a licensing point of view,
I've notified the NaCl SDK team and they'll look into revising the wording.

The statement "NaCl modules must be run from the Chrome Web Store (CWS)" is
a statement about what the browser permits without user action *by default*,
not a licensing statement.
It was meant to contrast with the statement above it regarding PNaCl
(portable native client), which the browser will by default load from any
page.
Users of Chrome or Chromium can opt into running NaCl modules on web pages
outside the Web Store from about://flags. Additionally Chrome Apps can be
side-loaded from the chrome://extensions page or at the command line.

The NaCl port of Emacs will run in both chrome and chromium.  While we do
plan to make a copy of Emacs available (for $0, and with a link to source)
in the Chrome Web Store, the web store is not a requirement, and can be
bypassed completely in several ways. The first is to "sideload" the app
from chrome://extensions (this is for example how I test local builds).
Chrome and chromium can also be run with the "--load-and-launch-app"
command line flag, which allows the user to load any chrome app from any
directory.  Additionally, we hope to eventually complete a PNaCl port of
Emacs.  In the default configuration of Chrome/Chromium, this will allow a
web page with part of the page running full emacs, downloaded on demand.

NaCl Emacs can be compiled today from the open source patches and scripts
in the https://chromium.googlesource.com/external/naclports.gitrepository,
and is being redistributed freely already.

Does this address you concerns?

On Mon, Mar 30, 2015 at 3:12 AM, Richard Stallman <rms@gnu.org> wrote:

> [[[ To any NSA and FBI agents reading my email: please consider    ]]]
> [[[ whether defending the US Constitution against all enemies,     ]]]
> [[[ foreign or domestic, requires you to follow Snowden's example. ]]]
>
>   > Thanks, I did a bit more reading about NaCl and in
>   > <https://developer.chrome.com/native-client> I ran across the
> statement "NaCl
>   > modules must be run from the Chrome Web Store (CWS)".
>
>
> I will take a look.
>
> --
> Dr Richard Stallman
> President, Free Software Foundation
> 51 Franklin St
> Boston MA 02110
> USA
> www.fsf.org  www.gnu.org
> Skype: No way! See stallman.org/skype.html.
>
>