As mentioned in #560, the following MWE will typeset the second frame (3 slides) with columns shifted to the right, as if the whole column is squished:
\documentclass{beamer}
\geometry{paperheight=2cm}
\begin{document}
\begin{frame}
\begin{columns}
\begin{column}{0.3\textwidth}
Column A
\end{column}
\begin{column}{0.3\textwidth}
Column B
\end{column}
\end{columns}
\end{frame}
\begin{frame}
\begin{columns}
\begin{column}<alert@2->{0.3\textwidth}
Column A
\end{column}
\begin{column}<structure@2->{0.3\textwidth}
Column B
\end{column}
\end{columns}
\end{frame}
\end{document}
As mentioned in #560, the following MWE will typeset the second frame (3 slides) with
columnsshifted to the right, as if the whole column issquished: