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What are you doing to remove the widows and orphan? As Kobo uses the default value of 2 for these, you want to set these to 1. I normally put it in the body class, but, sometimes leave it in the class used for the body text.
And even when you have it set to this, the space at the bottom depends on what is on the page. If it is all just text with the same class, and hence the same size and spacing, the space at the bottom will be consistent. And it will be room for less than one line.
But, on pages with other elements on it, such as a chapter heading or a scene break, then the amount of space at the bottom will be different. It should still be less than the space required for one line, but, the exact size will be different from the plain text pages.
Beyond those comments, we would need to see some examples. The book code and screenshots should help to tell what is happening.
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