The Unix idea has never been that text files are the best primitive, it's that they're the best approach
until you have a solid reason to do otherwise, and you should start simple. (Unix is more pragmatic than that - "worse is better", etc.) As long as you use plain text, you can use grep, diff, various version-control systems, etc., without having to rewrite any tools for your custom format. Still, sometimes you need more elaborate formats.
SQLite is one good example of a portable, open, simple format that is complementary to flat files. JSON and Lua also seem very Unix-y to me. Unix typically also uses ELF, various compiled key-value databases, etc.
Unix's choice of data types was also influenced by being written for computer that had 32k of RAM. That's, what, as much as a bar of soap nowadays?