The XS file from which you quote is xs/id3v2tag.xs (package Audio::TagLib::ID3v2::Tag).
There's also a declaration of TagLib::Tag::isEmpty() in xs/tag.xs (package Audio::TagLib::Tag) but no such declaration for the "header" function. I suspect this goes at least partway to explaining that isEmpty() can be loaded via package Audio::TagLib::Tag, but header() cannot.

Cheers,
Rob