1) Clicking on a bookmark link resets the user configured zoom setting
2) Page down should subtract at least 1 full line, preferably 2 or even 3 in order for th user to reorient themselves to the new page.
1) Acrobat Reader uses the zoom settings at the bookmark. It is not a bug.
That seems to me to be a very specific application that normal user cases would not want. How do I override this "feature" so that I can set an overall zoom for the entire document and be able to click on the Table of Contents at will without having to reset the zoom every time?
Let me explain. Under the normal use case, zoom is generally a function of the windows size and resolution of the monitor you are viewing the document in. It is, in general, not a property of the document or bookmark within a document.
This is at the discretion of the file's author. If they wanted the user to keep their preferred zoom setting they could have selected the Inherit Zoom option for the bookmarks they created. Either they didn't want that, or they were not aware of this setting, and have created bookmarks with a specific zoom setting. The application simply follows their directive.
You can't do anything to change it with the free Reader. You'd need Acrobat, or you could do it with an external tool, like this (paid-for) standalone tool I've created: https://www.try67.com/tool/batch-edit-zoom-level-in-bookmarks
You can change the settings of the bookmarks with Adobe Acrobat.