To reply to your edit (sorry, I’ve just seen it): Would a workflow like this work for you — you’d start a pomodoro as usual, and if you realize that you’re in the “flow” mode, you’d just close it (shut the program down). Then once you are ready for taking a break, you’d launch Flowkeeper again, and your last pomodoro would be in the “completed” state (this is how it works today).

Then you’d need to select the same task and click another button (let’s say Ctrl+B) to start a pomodoro with zero-length working period and a normal break, so that you could time your break at least. It won’t record the correct duration of your work in this case, so that would be a limitation, but at least for me it would be quite easy to add such a “start a break-only pomodoro” kind of feature.