Of course there are many options, but the benefit of the SQLite approach is the existing tooling, support, etc. Like others have said, one could just write a SQL interface over a set of virtual tables derived from the actual elf (if one just wanted a CRUD-like interface to a binary).

All of the benefits of SQLite disappear once one diverges from the format in any way. At which point it would be better to ask: "what is the best first-principles implementation of this idea?", instead of "what is the minimal change to SQLite to achieve this specific narrow goal?"

I might look at this next; with Nix it's easy to explore and rebuild seamlessly ;P