Driving in Japan is easier than you imagine it might be, though I would hesitate to drive in Tokyo. The car I rented in Hokkaido in 2016 had navigation in English (I had to specifically request this option when booking), and I needed an International Drivers Permit. The navigation interface was a little unusual relying on phone numbers or points-of-interest that people might want to visit - landmarks, schools, gas stations, etc. Though there didn't seem to be a way to enter a specific address, I found it quite easy to get navigation to some nearby POI, and then zoom in for the last few streets and use it like a regular street map.
The ETC card is for the (very expensive) highway tolls. I had to pay a small extra charge to rent the ETC card, but it gave a discount on the toll rates. In the end, the total discount I obtained was not much more than the rental cost of the ETC card, but it made dealing with the tolls a lot easier and allowed the car rental company to bill me immediately when I returned the car. The toll highways themselves are managed by a regional highway company and the one for Hokkaido had a website that let you calculate the toll for a specific journey - in my case, around $80 for 380km of highway driving! But note that not all stretches of highway are toll roads. The situation could well be a lot different for the highways around Tokyo.
However, perhaps you should compare the car rental prices from Ekiren: $60 or more per day, plus gas; with the price of taxis: around $3 per km. If you are not doing much driving around at your destination and just using it as a means to save a 5km walk, it could turn out to be cheaper taking a taxi when needed.