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.
Does this address you concerns?