I think one of the biggest problems I faced was honestly managing personal expectations and self-care. While finding PMF etc are hugely important, they're also difficult to do if you're not in the right mindset - meaning not only that you're thinking clearly and intelligently but also creatively. Managing time for exercise, friends and general relaxation proved more difficult for me during crazy startup times than any other job I've had.
To me this is most useful when you're doing something that doesn't take any thought or creativity. I use it for rote tasks that I don't want to do and find myself having trouble concentrating on. In general, I agree with the just wanting to get in the zone and not being confined to a timer, but when getting those awful tasks out of the way I do like this method.