No setting to disable the box. I've already sent an email to the app creator about this.
I did find a work around though - instead of dragging up to go to the next chapter you can tap in the left edge of the screen and it will advance the page - if you are at the end of the chapter it advances to the next chapter without the box. You must have "Edge tapping" enabled in "EPUB Book Settings/Vertical Scrolling Mode/". This works with auto-scroll either off or on.
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