Issue 1:
This will also be a problem if you put the page into categories, or feeds, etc. Since the page can have multiple containers at the same time, there will always be the possibility of the breadcrumbs not making sense. Really the best we can do here is create an option to choose which breadcrumbs are used for each page, as a page-level setting.
This is accepted as a feature request.
Issue 2:
Since you are having a problem of chapters appearing while the content list is filtered to Books only, make sure that you have not classified your chapters as Books too (Edit tab > Treat this page as). There are known bugs in beta with certain filters, but Books is not one of them.
Chapters don't need to be treated as books, unless you want to give them chapters too. In this case, the expected behavior is for the area to list everything that has been classed as a book. An area is just a generic box that contains content. It will not respect the book hierarchy -- that is what books do.
Since wiki content can have a number of classifications at the same time, filtering by one type does not rule out other types of content, but it shows us content that at least has the selected type. In order to achieve what you ask, a separate NOT filter would need to be added. In that case, you could choose to show only: Books, and also to not show: Chapters. This would net you high-level books. However, there would be no combination that shows mid-level books without high-level books.
The usefulness of such a feature would be limited. And it would open to the possibility, what if we want to show only: Books that are also Categories, or Show either: Books or Categories. Now we need another option for these, with its own, equally limited cases. By the way, it solves mid-level books without high-level books. (Show only: Books, That are also: Chapters).
The ability to select "That are Also" and "Do Not Show" filters are accepted as a feature request. Show Either requires too much work for certain fringe cases, and will not be handled at this time.
In the mean time, if you need nested books before these filters are added, and want to only show your high-level books in a content list, then you need to use a different strategy. Examples:
A) Use a Category instead, and only list the books you want in it. Link to the category in your area or index text, or only make the category area visible on the index.
B) Sort your area by Title, and make sure all titles in the same book start with the same letter/number. e.g. 123 Main Book > 123 Volume > 123 Chapter.
C) Move sub-books to another area (e.g. Books > Volumes > Chapters). Now your Books area will only contain the books you want.
You can already hide the contents of specific areas via permissions. So for usergroups who may not need to moderate the book area, you can turn off "Can view the list of area contents?" In the Area Manager, click the "Permissions" link for your Books area.