@rwhe,
I did try your epub but I'm not sure it's much help as my Kobo Glo is on fw3.0.0 (with Kobo Patcher mods).
FWIW, I drag-dropped it directly to the Glo and paged through most of the epub (as standard epub, not kepub) and I did not see any font-size changes between chapters, nor did the Adobe side page numbers show.
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