Is it possible to compare a funnel for two different versions of the product at the same time? for example, I would like to compare the funnel steps of the onboarding phase in our last two versions side by side
Not at the same time. A breakout can be added for various aspects, but app version is not one of them. You could, as a workaround, run the funnel once for each version, then download the csvs and compare offline. We'll add this as a feature request.