I also see this as translating to the toggl track integration. While this is also the case in Toggl, I think that the general idea that "break" time is not included in your actual time reinforces the idea that a break takes away from productivity and slaps of the idea that "I am not paying you to sit on the toilet" sort of mentality. If you were to have an uninterrupted 8 hour day and take a 5 minute break after every pomodoro with no large break, you would be only working 6 hours and 40 minutes in both Sunsama an Toggl. On all accounts, taking these breaks actually helps with productivity and should be considered as crucial parts to the working day. While subtle, having this setting disincentives taking breaks. If you were to "achieve" the sunsama goal of working 8 hous while doing the pomodoro method (sans the 30 minute breaks), then you would need to work almost 10 hours.

Yes! I'm having this issue too - I can't use the pomodoro timer reliably when timeboxing tasks because the breaks don't count toward the overall time on a task. It causes all my timeboxes to slip forward and ruins my schedule unless I do mental math to account for pomodoro breaks.