Move shaded polygon behind chemfig schemes
You could put it on a background layer, but why bother? Does it matter if it is behind? Or only that it looks as if it is behind? If the latter, what about the following?
\documentclass{article}
\usepackage{chemfig}
\begin{document}
%\schemedebug{true} % uncomment to see node names
\schemestart
P \arrow(P--Q){<=>[$\mathrm{k_{pq}}$]} Q
\arrow{<=>[$\mathrm{k_{qs}}$]}[30] S \arrow(S--T){<=>[][$\mathrm{k_{st}}$]}[-30] T
\arrow(@Q--R){<=>[][$\mathrm{k_{qr}}$]}[-30] R
\arrow(@R--@T){<=>[][$\mathrm{k_{rt}}$]}
\arrow(@T--U){<=>[][$\mathrm{k_{tu}}$]} U
\arrow(@U--V){->[$\mathrm{k_{uv}}$]} V
%
\chemmove{%
\draw [red,fill=red,fill opacity=0.5,blend mode=multiply,thick] ([shift={(-5pt,1em)}]Q.north west) -- ([yshift=1em]S.north) --
([yshift=1em]T.north) -- ([shift={(5pt,1em)}]U.north east) --
([shift={(5pt,-1.5em)}]U.south east) --
([yshift=-1.5em]T.south) -- ([yshift=-2em]R.south) --
([shift={(-5pt,-2em)}]Q.south west) -- cycle;
}
\schemestop
\end{document}
Just in case you really want it behind, there is always the eso-pic rescue.
\documentclass{article}
\usepackage{chemfig}
\usepackage{eso-pic}
\begin{document}
%\schemedebug{true} % uncomment to see node names
\schemestart
%
P \arrow(P--Q){<=>[$\mathrm{k_{pq}}$]} Q
\arrow{<=>[$\mathrm{k_{qs}}$]}[30] S \arrow(S--T){<=>[][$\mathrm{k_{st}}$]}[-30] T
\arrow(@Q--R){<=>[][$\mathrm{k_{qr}}$]}[-30] R
\arrow(@R--@T){<=>[][$\mathrm{k_{rt}}$]}
\arrow(@T--U){<=>[][$\mathrm{k_{tu}}$]} U
\arrow(@U--V){->[$\mathrm{k_{uv}}$]} V
%
% \chemmove{%
% }
\schemestop
\AddToShipoutPictureBG*{
\tikz[overlay,remember picture]{
\draw [red,fill=red,opacity=0.5,thick,semitransparent] ([shift={(-5pt,1em)}]Q.north west) -- ([yshift=1em]S.north) --
([yshift=1em]T.north) -- ([shift={(5pt,1em)}]U.north east) --
([shift={(5pt,-1.5em)}]U.south east) --
([yshift=-1.5em]T.south) -- ([yshift=-2em]R.south) --
([shift={(-5pt,-2em)}]Q.south west) -- cycle;
}
}
\end{document}
For the example at hand, @cfr's solution is probably simpler, but if the foreground has colors, this method might be considered.