There are a lot of SQLite praises in this thread, on the internet and on SQLite's website so here are a couple of reasons that drove me to choose it. My experience with traditional formats like CSV or raw binary is that they have a somewhat lower overhead to "get working" but are quite difficult to scale and adapt to changing needs, a phase most projects are bound to go through.

SQLite's reputation and adoption makes me comfortable to assume its operational correctness so I can focus on data itself, not reader/writer logics for it. Even though a SQLite database's schema may change, I'm glad knowing that the database file can still be easily opened and read many years into the future, something that custom formats may not guarantee.

On CSV: Syntax and library differences aside, SQLite almost works like a drop-in replacement for CSV since a single table database can be essentially treated as a glorified spreadsheet/CSV if wished. My post processing data pipeline is built with pandas so it is virtually the same for me to read a SQLite database vs. a CSV file.