As far as I can tell kepubs display 'chapter number/name – page x of y' as the standard page footer if:
- the current kepub content file has an entry in the TOC NCX file. The 'chapter number/name' label will match the NCX label for this content file. **
- Reading Settings: Display progress for: Current chapter
- Reading Settings: Display progress as: Page number
- As far as I'm aware it has nothing to do with any html TOC or Adobe Page Template. I have always removed both of these files from all my books before reading as part of my standard cleanup workflow.
** Note: This is true if your kepub was created from an EPUB2 source. If your source is an EPUB3 I don't know whether the labels come from the TOC NAV file rather than the TOC NCX. I can't easily test this because all my kepubs created from EPUB3 always have one-to-one matching NAV and NCX entries.
FYI: It is the calibre KoboTouchExtended driver which can be configured to do an on-the-fly format-shift (not a conversion) from epub to kepub, not the Kobo Utilities plugin.