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.

I cannot find a link, but I did see a discussion of this online, in GCC bug database.

The warning is issued on the actual delete expression. In the case of unique_ptr, the delete is called inside a system header file.

According to the discussion in that bug report, implementing C++ system libraries requires all sorts of compromises that result in various warnings. Therefore, the warnings are restricted inside system headers. That is the reason you won't see the warning you expect.

Update: and here it is, straight from the horse's mouth:

https://gcc.gnu.org/onlinedocs/cpp/System-Headers.html

The header files declaring interfaces to the operating system and runtime libraries often cannot be written in strictly conforming C. Therefore, GCC gives code found in system headers special treatment. All warnings, other than those generated by ‘#warning’ (see Diagnostics), are suppressed while GCC is processing a system header.