Indeed. You're definitely right on that point.
However, as I also mentioned, Chromium code includes unlicensed files, that
is to say nonfree files. This might be the important part regarding the
reason why chromium-browser is being removed by the trisquelize.sh script.
I think it has something to do with Chromium licenses.
Some licences (like Ms-PL or MPL) are GPL-Incompatible, according to FSF :
http://www.gnu.org/licenses/license-list.en.html
Furthermore, Chromium code includes unlicensed files i.e. nonfree.