What is omnibus?
An omnibus binds two or more volumes of a series into one physical book. A 3-in-1 is an omnibus. It counts as one book on the shelf and as a range of volumes in the story.
The mismatch is the whole problem. Naruto's 3-in-1 edition is 24 books. The singles are 72. Someone who owns the first omnibus owns one book and volumes 1–3 of the story. A tracker that only has a volume number cannot say which of those it means.
Hondana stores a volume range on every entry: start and end. A single uses the same number twice. An omnibus uses the range printed on the book. The obi, the coloured band, is only a label on top of that range. The range is the data.
Omnibuses are their own edition, not a view of the singles. Owning the omnibus does not mark the singles as owned. If you later buy a single because you want the cover, or you replace a 3-in-1 with singles, both can sit on the shelf without one deleting the other.
Related
See the words on a real set in the edition catalog.