siunitx uncertainty values - different number of decimal places (e.g. 98.5 +/- 0.98 %)

There are limits to what one can convince the parsing system to do: where that happens, you'll need to do things manually. Depending on how you want your markup to look, you might go with

\documentclass{article}
\usepackage{siunitx}

\begin{document}
\SI[parse-numbers = false]{98.5 \pm 0.98}{\percent}
\end{document}

or

\documentclass{article}
\usepackage{siunitx}

\begin{document}
$98.5 \pm \SI{0.98}{\percent}$
\end{document}