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If Foliate does not use the NAV when properly specified in the OPF manifest, then it simply is not an epub 3 compliant reader. It probably just supports epub 2. Older readers like that are why some epub devs include a fully parallel NCX and OPF guide in their epub 3s to make them more compatible with old epub2 only readers.
Perhaps a good epub3 reader that handles epub2 would be an improvement. If so try Thorium. It exists for Windows, Mac, and Linux desktops and is very spec compliant.
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