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The difference between Sigil 1.9 and Sigil 2.0 is likely due to the different QT version using and how it handles combining glyphs.
Since the Uthman font does seem to have the characters you want in the Arabic Presentation area ( specifically U+FC00 to U+FD1D and U+FD50 to U+FD7D ), it might be worth trying to use those glyphs directly. I generated the hex font names and dumped them into your test epub. Oddly, when I did a mend and prettify, the glyphs displayed in the Sigil code view do not match those glyphs when seen in Preview but do have some semblance to the components of the glyph shown in FontForges Glyph Info => Components.
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