I am responding to a question about MS Word. I know nothing significant about ebook publishing protocols.

The automatically generated table of contents uses different styles to generate each level of the TOC depending on the level of the source. These are normally set as you insert the TOC. You can change these style definitions, though if needed.

I would recommend, in a copy, trying to re-insert your TOC with different looks. Otherwise you can change the styles. The right margin you are observing is actually a right-tab setting in the style for the page number (often with a dot leader). Here are some references that might help.

How to create a table of contents in Microsoft Word
Complex Documents