[Quoth]

<br/> Appears automatically in my chapter headings if I do newline rather than regular enter (which makes a new paragraph) so as to force a two line heading rather than random wrap.

It means any auto TOC generation only has one entry for the chapter rather than two; the renderer auto spaces the two lines according to the font metrics/size.

But I can't think of any other situation that uses <br/> that's not better done some other way. Again the goal is to not edit the ebook, but only source, the exception being tweaking CSS for images.

I also run search & replace on the WP source so that:
There are only single spaces ever.
No leading spaces
No trailing spaces.
No empty paragraphs
(In LO, $[ ], [ ]^ and ^$)

You'd have to deliberately type a newline as "enter" is always a new paragraph.