I don't see why we should abandon that for the convenience of somebody's evidently-nonstandard Python build.
The proposed patch also breaks the header isolation that the separate plpython_system.h header is meant to maintain. Arguably we should have #define'd Py_LIMITED_API inside plpython_system.h, not where it is. But I don't feel a need to mess with that without a far better argument for why we should change this at all.