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There are spurious spaces in the definitions (imho it is not really a good idea to use \setbeamerfont in this place. Fonts should be setup in the preamble).

\documentclass{beamer}
\newcommand{\mytinyfootnote}[1]{%
   \setbeamerfont{footnote}{size=\tiny}%
  \footnote{#1}%
}
\makeatletter
\renewcommand\beamer@clearbeamerfont[2]{%
  \def\beamer@temp{#1}%
  \setkeys{beamerthm}{size={},shape={},series={},family={},parent={}}%
  \setkeys{beamerthm}{#2}%
}

\renewcommand\beamer@setbeamerfont[2]{%
  \def\beamer@temp{#1}%
  \setkeys{beamerthm}{#2}%
}

\begin{document}
\begin{frame}
  \begin{itemize}
  \item \tracingoutput=1 Foo\mytinyfootnote{Bar}
  \item Foo\footnote{Bar}
  \end{itemize}
\end{frame}
\end{document}