I think it'll work even with whole-book page numbering turned on, if you give MapleRead enough time to finish the page numbering background process. When it's done, the (whole-book) percentage displayed turns into a page number.
Note that this whole-book page numbering business actually counts the real number of layout-dependent (including font size) pages like iBooks. Many other apps support only ADE page numbers, which basically just count the number of characters, regardless of layout, which thus may give you the same ADE page number when you "flip" to the next page.
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