Read the original relational database paper by Codd. The problem is that trees of data are not flexible for querying, you really need a graph. If you draw it out on paper, you will find a relation is a very efficient way to store general graphs. I'm actually suprised to hear this from a C++ engineer, because sorting and searching columns of data is the name of the game in C++.

Another key problem they solve is separating the logical representation from the on disk representation. You can evolve and and optimize storage without breaking anything.

The other problem with files is that you have a disconnect between in memory and on disk. You have to constantly serialize and deserialize. Sqlite has quite a bit of info on this: https://www.sqlite.org/appfileformat.html