std::unique_ptr of base class holding reference of derived class does not show warning in gcc compiler while naked pointer shows it. Why?

Well, first of all, deleting a derived object through a base pointer when the base class does not have a virtual destructor is undefined behavior. Compilers are not required to diagnose undefined behavior…

That being said, the reason why this warning does not appear when using std::unique_ptr is most likely due to the fact that GCC does not report warnings that would appear in system headers.