So, as I understand it, for the first scenario, you'll want to make sure the "all inclusive plate pass fee" is added to your rental at the time of rental. This is was added as $25.99 to my rental yesterday at EWR.

We'll see if there are any hiccups but as I understand it, I should not have to pay the individual tolls. I would have gotten my money's worth if I had more time as I originally wanted to cross the Verrazano bridge but as it went, I probably got close to the fee if not exceeded it with the bridge crossing into Staten Island and several other tolls.

I only took this option bc I forgot to bring my iPass but I think this worked out for this trip.

The key to this package is it has to be added on before. Otherwise, you apparently will get charged the daily fee for plate pass (less than the all inclusive fee) and pay all the tolls.

In your second scenario, you probably want to have your own EZ pass or equivalent. You could add on the all inclusive at star of your rental but you'll be paying $26 every day of the rental. Or you pay the plate pass daily fee for every day of the rental (including says you don't have any tolls) plus the tolls themselves.
Edit:
I only had this car one day. I'm actually wondering what I'd do for future trips that are longer. I would kinda want to see if I could break up a trip. I want to visit relatives in the NY and DC area and also see some of New England. Maybe the way to do it would be to get rental for several days that makes heavy use of tolls and then get another rental for when I don't need to use a lot of toll roads.