Hi Shai- Julianne from Mixpanel Support here.
Diving right in, the exact funnel behavior is impacted by the conversion criteria as well. But at a high level, an event comparison isn't necessarily expected to match a breakdown.
When you use event comparison, Mixpanel essentially creates two separate funnel reports in a single view. For example, if you're comparing layout 1 and layout 2, Mixpanel will create one funnel for users who did layout 1 and another funnel for users who did layout 2. If a user tracked 'View Screen' with both values, they could enter both funnels.
With a breakdown applied, a user can also enter each segment, but only after having exited the previous attempt (ie, via converting or timing out).
As an example, let's say a user tracks the following, all within the conversion window:
1. View screen, layout = 1
2. View screen, layout = 2
3. Subscribe to plan
With the event comparison funnel, the user would enter and convert for both layout 1 and layout 2. With the breakdown funnel, the user would enter on Event 1 with layout = 1. Since they haven't exited that funnel attempt, Event 2 would be ignored in the funnel. This means the funnel would show one conversion for layout 1 and no conversions for layout 2.
Let me know if you have any questions!