Avoid bfseries from bolding \pm in siunitx

You can also use the b font series so the numbers will have the same size.

\documentclass{article}
\usepackage{siunitx,etoolbox,booktabs}

\sisetup{separate-uncertainty}

\begin{document}

\begin{table}

\centering
\renewrobustcmd{\bfseries}{\fontseries{b}\selectfont}
\renewcommand{\pm}{\mathbin{\mbox{\unboldmath$\mathchar"2206$}}}

\begin{tabular}{
  c
  S[detect-weight, table-format=-1.1(1),mode=text]
}
\toprule
Header1 & {Header2} \\
        & {Sub} \\
\midrule
A2          & -6,2 \pm 1,3 \\
A3          & 4,8 \pm 1,7 \\
A7          & \bfseries 5,7 +- 2,0 \\
A12         & 5,9 \pm 2,1 \\        
\bottomrule
\end{tabular}

\caption{Caption.}
\label{table:mwe}

\end{table}

\end{document}