I suspect you won't get an answer on this forum from anyone who's actually booked a Q-Tour.

The Romance Car surcharge is 1,150yen from Shinjuku to Hakone Yumoto

Much of the accommodation you can book yourself in Hakone will include dinner and breakfast.

The freepass includes discounts for many of the area's sightseeing attractions.

You may want to contact Q-Tours yourself to find out what entrance fees their package does cover. From the Shunkoso example, it would need to be over 8,000yen to make it worthwhile - there are only so many Art Galleries/parks you can visit in two days... Sorry, hclee01, you seem to be much more interested in this package than anybody else who posts here, I can see no reason for me to want to delve any further.