After installing avr-gcc, I cam confirm this issue.
If the compiler-plugin detects the gnu-avr-gcc compiler it adds /usr/include and /usr/lib to the appropriate search dirs, but this is (of course) wrong for a cross-compiler.
I guess none of these is normally needed as long as only compiler-included headers and libs are used, because the compiler normally knows where to search.
I am not sure if it is needed on windows, normally it should not.
The wrong search-dirs are only added, if auto-detection does 
not fail:
    AutoDetectResult ret = wxFileExists(m_MasterPath + sep + _T("bin") + sep + m_Programs.C) ? adrDetected : adrGuessed;
    if (ret == adrDetected)
    {
        if (platform::windows)
        {
            AddIncludeDir(m_MasterPath + sep + _T("avr\\include"));
            AddLibDir(m_MasterPath + sep + _T("avr\\lib"));
            m_ExtraPaths.Add(m_MasterPath + sep + _T("utils") + sep + _T("bin")); // for make
        }
        else
        {
            AddIncludeDir(m_MasterPath + sep + _T("include"));
            AddLibDir(m_MasterPath + sep + _T("lib"));
        }
    }
 m_MasterPath is 
/usr, because the executables are in 
/usr/bin as nearly in all cases on linux.
That's the cause, why I did not see them until I installed the compiler.