Thanks for the observation. I noticed that earlier too, and saw the FAQ provided in their website as follows:
1. Difference between Freepass and Q-Tours
Q-Tour includes roundtrip transportation ticket (including Romancecar) to and from Shinjuku Station, meals, sightseeing entrance fees, and hotel fare. Tourists can save their time by not having to buy separate tickets for trains, buses, ships, etc. This tour is particularly convenient for tourists who do not have enough time to make individual travel arrangements (the tour course is fixed). Since Freepass is only a transportation ticket, guide book, meals, etc. are not included.
So besides the meal, romancecar, accomodation, what else is covered in Q-Tour and not in Freepass? What entrance fees are being covered in Q-Tours?