I use https://kanbanflow.com/. I can have a list of things I want to get done in a day, and when I finish one task I can switch to the next one in the middle of a pomodoro. (The pom timer is at the bottom of the page)
If I'm on a roll and the timer ends, then yes I extend my pom longer because I don't want interrupt that. A lot of the time I don't need to, and can pick up just were I left off after my five minute break.