They're a corporation. Some of their decisions are made accordingly. The most interesting bits, though (version controlled dumps of the LaTeX you're working on) do have open implementations.

Ultimately, it (like Paperpile) is a service that is built from mostly open components, integrates nicely with OA workflows, and has no real lock-in. I'm not sure what you're afraid of -- a paper will unsubmit itself? LaTeX will go closed source? Since your entire version history is there for the taking at any time, there's not much downside, and for our manuscripts & tech reports we've seen huge upside.

Ymmv!