Imagine that I want to do at least three sets of pushups spread throughout the day.
I can set up an action "do set of pushups at least three times every day".
Now imagine that I failed to do three sets yesterday and, by late afternoon, have done two sets today. My dashboard might look something like the following:
Notice that the priority score for Today is 200 and is colored red, indicating overdue. This is because we missed yesterday.
However, we're on track to hit our target of three sets today. The green 74 under Now indicates the priority of doing another set right now. We still have a decent amount of time to do one more set which is why the priority is green. As we approach midnight, the number will increase. If by 5.52pm we hadn't even started our pushups yet, habitualist would give a Now priority over 100 and colored red because we're off pace for today.
The apparent discrepancy in priority is most evident with actions that are to be done more than once per period. One way to think about it is Today indicates the priority of completing the required number of repetitions of the action by the end of the day; Now indicates the priority of completing one more repetition of the action right now.
As we add more flexibility in specifying when you'd like to do an action, the subtleties will likely increase but hopefully this clarifies things.