The question reads like an XY problem, they describe DB functions for data structures so unless there's some specific reason they can't use a DB that's the right answer. A "spreadsheet for data structures" describes a relational database.
But they need rectangular structure. How do they work on tree structures, like OP has asked?
Relationships. You don't dump all your data in a single table. Take for instance the following sample JSON:
You'd structure that in SQL tables something like this:
The dbo.favorites table handles the many-to-many relationship between users and games; users can have as many favourite games as they want, and multiple users can have the same favourite game. The dbo.platforms handles one-to-many relationships; each record in this table represents a single release, but each game can have multiple releases on different platforms.