How to put horizontal space between two side by side figures, then automatically scale the pictures to that new width?

\documentclass{article}
\usepackage{graphicx}
\usepackage{caption}
\usepackage[paperwidth=6in, paperheight=9in, margin=0.9in, showframe]{geometry}
\usepackage{lipsum}
\begin{document}

\begin{figure}
\centering
\begin{minipage}{.4\textwidth}
\centering
\includegraphics[width=1\linewidth]{example-image}
\end{minipage}\qquad
\begin{minipage}{.4\textwidth}
\centering
\includegraphics[width=1\linewidth]{example-image-golden-upright}
\end{minipage}

\bigskip

\begin{minipage}[t]{.4\textwidth}
\centering

\caption{an evergreen eastern Asian shrub related to the tea plant, grown for its showy flowers and shiny leaves.}
\label{camellia}
\end{minipage}\qquad
\begin{minipage}[t]{.4\textwidth}
\centering
\caption{a prickly bush or shrub that typically bears red, pink, yellow, or white fragrant flowers, native to north temperate regions. Numerous hybrids and cultivars have been developed and are widely grown as ornamentals.}
\label{rose}
\end{minipage}
\end{figure}

\lipsum
\end{document}

Just reserve the wanted space to the minipages; with \dimexpr it's easy to fix the space in between the images (here to 2 ems).

Note that you don't need \captionof. With \begin{minipage}[t] you ensure alignment with respect to the bottom of the pictures.

\documentclass{article}
\usepackage{graphicx}
\usepackage{caption}
\usepackage[paperwidth=6in, paperheight=9in, margin=0.9in, showframe]{geometry}
\usepackage{lipsum}
\begin{document}

\begin{figure}
\centering
\begin{minipage}[t]{\dimexpr.5\textwidth-1em}
\centering
\includegraphics[width=\textwidth]{example-image-9x16}

\caption{an evergreen eastern Asian shrub related to the tea plant,
grown for its showy flowers and shiny leaves.}\label{camellia}
\end{minipage}\hfill
\begin{minipage}[t]{\dimexpr.5\textwidth-1em}
\centering
\includegraphics[width=\textwidth]{duck}

\caption{a prickly bush or shrub that typically bears red, 
pink, yellow, or white fragrant flowers, native to north 
temperate regions. Numerous hybrids and cultivars have been 
developed and are widely grown as ornamentals.}\label{rose}
\end{minipage}
\end{figure}

\lipsum
\end{document}