Refer to last slide (build stage) in overlay specification

This is actually a very tricky question -- highlighting something on the last slide of a frame is easy to do (you can calculate the total number of slides from frameendpage-framestartpage), but if I understand your question correctly, you don't want the highlight on the last slide of the frame, but on the one after it. This means an additional overlay has to be created and this changes the number of slides in this frame which would mean that in the next run the last slide is no longer the last slide .......

A way out from this dilemma is to create the additional overlay manually:

\documentclass{beamer}

\newcounter{foo}

\begin{document}

\begin{frame}
  \begin{itemize}[<+->]
    \item A
    \item 
        \setcounter{foo}{\insertframeendpage}
        \addtocounter{foo}{-\insertframestartpage}
        \addtocounter{foo}{1}
        \alert<\thefoo>{B}   
    \item C
    \item D 
  \end{itemize}
    \only<+>{}
\end{frame}

\end{document}