I don't know what metadata entries the questioner is referring to, but there are indeed some that don't show up in the MetaData Editor window.
The best example would be the standard meta entry with Sigil version. In EPUB2 it is visible, but in EPUB3 it is no longer.
Code:
<meta name="Sigil version" content="2.6.0"/>
Similarly, any other entry with this structure, such as
Code:
<meta name="beckyid" content="BeckyLibrary-1234" />
Such an entry, however, officially (I think) cannot be obtained directly in the MetaData Editor window for an EPUB3 file, although in EPUB2 it can be done without a problem.
I'd be happy to read what entries @PurplePassion has made, as the key here is not just the metadata entry itself, but also whether such entries pass EpubCheck validation.