Okay, it took some digging but I added my epub to Books.app on macOS and the cover appeared nicely on the BookShelf.
Then had to dig for the book in
~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books/
And then they had changed the name and unzipped it so it took some searching to find the book I wanted:
~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books/F7D7F8CBFC7F4D758B7DA0F1189703B3.epub
And that was a FOLDER and not an epub file. But inside that folder there was created:
iTunesMetadata.plist
and that file specified the cover image path:
Code:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>artistName</key>
<string>Gerhard Wiedmann</string>
<key>book-info</key>
<dict>
<key>cover-image-hash</key>
<string>1D8E173E5E63BB1ED6D5BE87D439D0C0</string>
<key>cover-image-path</key>
<string>OEBPS/Images/cover.jpg</string>
<key>mime-type</key>
<string>application/epub+zip</string>
<key>package-file-hash</key>
<string>F7D7F8CBFC7F4D758B7DA0F1189703B3</string>
<key>publisher-unique-id</key>
<string>urn:uuid:3851b112-6f3b-405e-bdba-2c00553c740d</string>
<key>unique-id</key>
<integer>8183410303695295555</integer>
<key>update-level</key>
<integer>2</integer>
</dict>
<key>genre</key>
<string>Non-Fiction</string>
<key>itemName</key>
<string>Memoirs</string>
<key>playlistName</key>
<string>Memoirs</string>
</dict>
</plist>
I would assume that Books.app on your iPad is doing something similar.