Book your car rental through Rakuten travel. There are uaually lots of deals. The car rental site is in Japanese only so use Google translate. I booked a 5 days rental for 300k yen (mid size) from budget car rental on Rakuten. A compact car will be cheaper.
I did check around and they are not that much cheaper, plus Toyota at CTS opens until 23.00 which is a huge plus when my flight was 8am.
300k yen for 5 days is pretty expensive, even Toyota doesn't cost that much. Toyota was the most lax when during car check upon return.
Overseas Fairfield doesn't include breakfast and whether they extend it to elite is entirely up to the hotel - one more reason to stay away from Marriott when in Japan.