You need to change the frametitle template *before* the frame starts:

```
\documentclass[xcolor={rgb}]{beamer}

\setbeamertemplate{frametitle}[default][center]

\usepackage[many, listings]{tcolorbox}

\usepackage{tikz}


\usetikzlibrary{arrows.meta,
	shapes,
	tikzmark}

\begin{document}

\begin{frame}[t]
\frametitle{First slide}
empty

\end{frame}

{
\setbeamertemplate{frametitle}[default][left]
\begin{frame}[t]
\frametitle{Bumps into the tcolorbox if not aligned left}
\addtolength{\leftmargini}{-0.7cm}
\tikz[remember picture, overlay]%
\node[inner sep=0pt, anchor=north east, shift={(-0.1cm,-0.5cm)}] at (current page.north east) {%
\begin{tcolorbox}[width=2.9cm,
boxsep=0pt,left=0pt,right=0pt,top=1pt,bottom=1pt,
    colback=blue!10,
    colframe=blue,
    coltext=black,
    halign=center,
    valign=center
]
    \small Some limited amount of text explaining an important thing.
\end{tcolorbox}};
\end{frame}
}

\begin{frame}[t]
\frametitle{Last slide}
empty

\end{frame}


\end{document}
```

![document-2.png](/image?hash=429ab42ba427c10fa479280ae356fed0dd9b6223cdc9b384c9e8657ffb8174f7)