World Heritage Pass to Nikko

I am aware that the World Heritage pass covers admission to the shrines and temples in Nikko. However, as I am reading through the site, I noticed the shrines and temples often have a base ticket price and also another fee you have to pay to visit some of its buildings. Like for example, an addition 520 yen has to be paid at the Toshogu Shrine to view the carving and the tomb. I was wondering if the World heritage pass covers these expenses.

And also, if I am think of visiting both the Shrines and also Chuzenji over a weekend, while staying near Kinugawa Onsen, it is cheaper to get the All Nikko Pass or the World Heritage Pass?

I noticed the shrines and temples often have a base ticket price and also another fee you have to pay to visit some of its buildings.

Often? I can think of only one case (and a second minor one):

In case of the Toshogu, a separate payment is necessary to see the carving of the sleeping cat and the tomb. It is not included in the World Heritage Pass (nor the 1000 yen combination ticket).

The minor case is the small Japanese garden and treasure house of Rinnoji, which is not included in any of the combination tickets except those bought at Rinnoji.

And also, if I am think of visiting both the Shrines and also Chuzenji over a weekend, while staying near Kinugawa Onsen, it is cheaper to get the All Nikko Pass or the World Heritage Pass?

World Heritage Pass: you save 1000 yen because admission is included, but you have to pay the bus ride to Lake Chuzenji separately. The best way to do that is by a 2-day pass for the buses which costs 2000 yen (if you go as far as the lake) or 3000 yen (if you go as far as Yumoto).
TOTAL: 5600 to 6600 yen (depending on how far you go into the Okunikko region)

Nikko All Pass: the pass is you have to pay an additional 1000 yen for admission to the shrines and temples, but the buses are fully covered.
TOTAL: 5400 yen

So, as you can see, the Nikko All Pass is the better value even if you travel only as far as Chuzenjiko.