It's not the best article to start a discussion like this because it's one-sided and a bit ignorant. But it wouldn't be fair to comment on it further here on hashnode.
To your question. IMO, yes, front-end is a separate application to me. Because... We are in the middle age of micro services (we know them since years but called them SOA not long time ago) and one service is about UI. To me, it's not React+Flux alone which helps to shape the future of front-end. It's the community thinking about how ES6/ES7, TypeScript, Elm, etc., you name it, can be used to ease things up or get rid of simple awkward tasks.