Tried it out, bought a copy :)
The thing i'm noticing most (and i can hack around this probably) is that there are some things that are productive in certain contexts (monitoring twitter after launching/announcing a thing) and not in others not (twtittering while i'm supposed to be writing code, or letting myself get distracted by twitter while waiting for something to build).
Would you consider some notion of rule sets scoped to some notion of "what i'm supposed to be doing"?
It will be hard to implement since the "smallest tracking unit" is activity - a website or a window. I also can't see how to implement it without making everything too complex (the app's UX is too complex already in my opinion).
You can try to use a different browser since domains are bound to browsers. Like using productive Twitter in Safari and distracting Twitter in Opera.
So, I honestly wouldn't change anything about the interface, except to wrap the entire thing in an outer shell with something that represents what GTD software might call a context.
And depending on context, different rule sets apply. Anyway, that's just a suggestion, don't mean to stomp on your notion of product, what you've got is a great start and a neat coupling of product experience and interesting engineering!
I especially like the ambient info display in the app icon. Seeing whether the app is bordered in green or blue every time i tab up the app switcher is a great piece of design.