Adding an unrecognized library with -I flag is 99.999% of the time the wrong way. The includes will be visible but the .cpp/.c files will not be compiled and you get exactly “undefined reference to <symbol>” errors.
If you have added the pmbtools to the lib_deps, are referencing the library directly in an #include statement in your source files but it still won’t show up, it may be because the library dependency finder find the library to be incompatible due to framework or platform restrictions declared in the library.json or library.properties. Set
lib_compat_mode = off
(docs) in the native environment to test that.