Q:

siunitx: some options must be in preamble, not with S[?

This is my question for siunitx users: Is it necessary to specify the input-symbols parameter in the preamble, rather than within S[]? 
Why do I ask?
Here's a table produced by my R function outreg in the package rockchalk. 
\documentclass[11pt,letterpaper,english]{extarticle}   
\usepackage{booktabs}
\usepackage{dcolumn}
\usepackage{array}

\usepackage{siunitx}
%following now in each table
\sisetup{
  input-symbols = ( )
}

\begin{document}
\begin{table}
\caption{Still have showAIC argument, as in previous versions}\label{tab:ex5ds}
\centering\begin{tabular}{@{}l*{2}S[input-symbols = ( ),   
                        group-digits = false,   
                        table-format = 3.3,
                        table-number-alignment = center,   
                        table-space-text-pre = (,  
                        table-space-text-post = {***},   
                        table-align-text-pre = false,
                        table-align-text-post = false,
                        parse-units = false]@{}}
\hline
   & \multicolumn{1}{c}{Whichever}& \multicolumn{1}{c}{Whatever}\tabularnewline
 & \multicolumn{1}{c}{Estimate}& \multicolumn{1}{c}{Estimate}\tabularnewline
   & \multicolumn{1}{c}{(S.E.)}& \multicolumn{1}{c}{(S.E.)}\tabularnewline
 \hline
 \hline
  (Intercept)    &403.245*** &29.774*** \tabularnewline
     &  (0.618) &  (0.522)\tabularnewline
  x1      &1.546*& \multicolumn{1}{c}{\phantom{000}.} \tabularnewline
     &  (0.692)   &  \tabularnewline
  x2     & \multicolumn{1}{c}{\phantom{000}.} &3.413** \tabularnewline
       &   &  (0.512)\tabularnewline
 \hline
 N& \multicolumn{1}{c}{100}& \multicolumn{1}{c}{100} \tabularnewline
 RMSE            &6.121  &5.205   \tabularnewline
 $R^2$            &0.048  &0.312   \tabularnewline
 adj $R^2$        &0.039  &0.305   \tabularnewline
 AIC     &617.694 &617.694\tabularnewline
 \hline
\hline

 \multicolumn{3}{l}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
\end{document}

Thanks to the help of members in this group, the output is mostly adequate, IMHO. I cannot know ahead of time how many digits might be used, so I don't rely on table-format to tighten down the alignment. That's why I've got the nagging problems about centering of different sections of table. But this is, honestly, much better than I had before. 
I'm asking now about the preamble and sisetup. I want the table markup to be as close to portable as possible, not depending on any preamble details.
I wanted to eliminate entirely the use of sisetup, but if I remove that from this example, it does not compile because the parentheses are not understandable to the compiler:
! siunitx error: "invalid-number"
!
! Invalid numerical input '(0.618)'.
!
! See the siunitx documentation for further information.

Is the preamble sisetup the only correction? 

A:

Your syntax of the tabular preamble is faulty. You are using *{2}S[...] But you should put braces around the second argument so that the optional argument of S is processed too:
\documentclass[11pt,letterpaper,english]{extarticle}
\usepackage{booktabs}
\usepackage{dcolumn}
\usepackage{array}

\usepackage{siunitx}
%following now in each table
\sisetup{
 % input-symbols = ( )
}

\begin{document}

\begin{table}
\caption{Still have showAIC argument, as in previous versions}\label{tab:ex5ds}
\centering\begin{tabular}{@{}l*{2}{S[
                        input-symbols = ( ),
                        group-digits = false,
                        table-format = 3.3,
                        table-number-alignment = center,
                        table-space-text-pre = (,
                        table-space-text-post = {***},
                        table-align-text-pre = false,
                        table-align-text-post = false,
                        parse-units = false
                        ]}@{}}
     &  (0.618) &  (0.522)\tabularnewline
 \end{tabular}
 \end{table}
\end{document}

