This is showing the libraries in the PlatformIO sense. If you manually add a statically linked library via the build_flags, PlatformIO doesn’t recognize it. It would count it however if it were inside a proper library folder within lib/.
Wrong folder structure, you need to have `lib/pd_open_library/< the .a and the .json file>. See the reference tutorial I linked above which has

The paths in here must be relative to the library folder, not the root project folder. Doing a simpler
"build": {
"flags": [
"-L.",
"-llibPDlib.a"
]
}
should suffice in this case. (The library is automatically added to the include path, so no -I is needed)