So it's deliberate, then? It seems odd to deliberately exclude them. Your decision, of course
IMO it can be quite useful to have a ToC entry for a map as you may want to keep referring back to it whilst reading. I suppose it's easy enough to create a bookmark as a workaround.
Lots of books do include a ToC entry for the main cover. In fact it may even be desirable for Kobo users as, for some strange Kobo-reasoning, newly opened epubs open at the location of the first ToC item (there are frequent complaints about this on the Kobo forum). Still, I understand it's not calibre's job to fix everybody else's quirks.