Feel free to skip APP_LIBS_LIST and USER_LIBS_LIST from Makefile and add them to Project > Project > Build Settings > User-Defined.
The real challenge is to obtain documentation about Xcode inner structure and keywords to improve:
- the template sets the sketch as c++ code and not plain text, for code-sense
- the template populates the Sources List for code-sense
- instead of having the serial console in a separate Terminal window, integrate it in Xcode debug pane
- ...