Yeah, but apps have a two pages mode for this, the content shouldn't join them by default. There are lots of people reading manga in double page mode and using the panel by panel feature without problems, they just have content that has the right format.

1 file per page doesn't mean you need to read page by page, you can enable the two pages mode and the app will display them as spreads, and then the reading order of the panels in panel by panel mode will be fine.