I don't think the page number shown depends on the font size. It doesn't change when you change font size, and if you're reading with a larger font, it can stay on the same page number for more than one page turn. However the page number shown doesn't always correspond exactly to any pre-defined page numbers in the book.
In any case, the page number could depend on a lot of things, but it's still not that difficult to implement a go-to-page-number function. You see a page number at the bottom of the screen. That's the one you want to go to. The Kobo firmware manages to keep track of it while reading, and it knows how many pages there are in the book. Even if were impossible to calculate the exact location of some arbitrary page number in the book, it could simply page forward fast from the beginning of the book with no display to arrive at the right page in a few seconds, or it could page forward or back from the current page (again with no display) to get to the right page faster.
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