I am not seeing that behaviour.
When I open the font settings, the page buttons still turn the page. To use them to adjust the font or other settings, I have to tap the control. Once I do that, the size/margins/line spacing changes when I press the buttons. After this, when I tap the text, the reading settings are closed and the page turn buttons work as expected to turn the page.
I tried the above with both epubs and kepubs.
This is with firmware 4.25.15875 which is the latest release.
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