update, so I took a quick look at the epub , no images version of that book
each para begins with this construct, where the id values are all different
p id="id00416"
I would use find and replace to take those about and to substitute class="bodytext",
then define bodytext in the CSS to have your preferred margins, indents....
so each paragraph would then look like <p class="bodytext"> some text <\p>
NB if you run a calibre epub to epub conversion, calibre will add class statements for you, which you can then redefine
i strongly suspect it the repetitive ID= that cause the issue, because most books do not have those in every paragraph; and also that it only affects/confuses the kobo . that other readers would remember reading position OK.
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