This is a choice the maintainers did on purpose (see the changelog for further information).
And there's _no_way_ to circumvent this: you can't put your --enable-remote-extensions flag in /etc/chromium.d/: it doesn't work, you'll have to start your browser from the command line for the foreseeable future. Having someone making choices in my behalf always irritated me. And I really don't think Debian users are so unwary.
