Yes, for now the approach is to provide simple programmatic interfaces over CMake and friends to make third party stuff easy to integrate. For example, SQLite:

  spn_autoconf_t* ac = spn_autoconf_new(dep);
  spn_autoconf_add_flag(ac, "--disable-tcl");
  spn_autoconf_run(ac);
  spn_make(dep);

That being said, I'll have a go at sel4 with the native build system. I use it for all my C projects already. Nothing tastes better than dog food, after all!