tikz - positioning pics just like a node

I think this question came up before. The trick is to wrap the pic in a matrix node (to be clear, this is a 1x1 matrix). This works unless you want to put the pic in a matrix, but there you can use the pic itself, or want to use a matrix in the pic, at least as of now.

\documentclass[tikz,border=2mm]{standalone}
\usetikzlibrary{positioning}
\tikzset{
pics/mypic/.style={code={
        \tikzset{mypic/.cd,#1}  \def\pv##1{\pgfkeysvalueof{/tikz/mypic/##1}}%
        \edef\m{\pv{m}}%
        \foreach \row [count=\j] in \m  {
            \foreach \r/\g/\b [count=\i] in \row {
                \fill[fill={rgb,255:red,\r; green,\g; blue,\b}] (\i-1,\j-1) rectangle ++(1,1);
            }%foreach
        }%foreach
    }},mypic/.cd,m/.initial={{255/0/0}},/tikz/.cd,
%
}
\begin{document}
    \begin{tikzpicture}
    \tikzset{
        box/.style={draw,minimum width=1cm,minimum height=1cm}
    }
    \def\clst{
{31/18/12}%
    }
  \node[box] (A) at (0,0) {A};
  \foreach \pos in {left,right,above,below} {
    \node[\pos=1 of A,matrix] (B-\pos) {\pic{mypic={m=\clst}};\\};
  }

\node[left=6 of A,box] (C) at (0,0) {C};
\foreach \pos in {left,right,above,below} {
    \node[\pos=1 of C,box] (D) {D};
}
    \end{tikzpicture}
\end{document}

One simple way of dealing with larger pics is to count the entries and making them symmetric.

\documentclass[tikz,border=2mm]{standalone}
\usetikzlibrary{positioning}
\tikzset{
        % colmat
pics/colmat/.style={code={
        \tikzset{colmat/.cd,#1}  
        \def\pv##1{\pgfkeysvalueof{/tikz/colmat/##1}}%
        \edef\m{\pv{m}}%
        \foreach \row [count=\j] in \m  {\xdef\mydimj{\j}
            \foreach \r/\g/\b [count=\i] in \row {\xdef\mydimi{\i}}}
        \typeout{\m,\mydimi,\mydimj}
        \edef\w{2}%
        \foreach \row [count=\j] in \m  {
            \foreach \r/\g/\b [count=\i] in \row {
                \fill[fill={rgb,255:red,\r; green,\g; blue,\b}]
                 (\i*\w-\mydimi/2,\j*\w-\mydimj/2) rectangle ++(\w,\w);
            }%foreach
        }%foreach
}},colmat/.cd,m/.initial={{255/0/0}},/tikz/.cd,
    %
}
\begin{document}
    \begin{tikzpicture}
    \tikzset{
        box/.style={draw,minimum width=1cm,minimum height=1cm}
    }
    \def\clst{
        {200/10/10},
        {10/10/200},
        {10/200/200}%
    }
    \node[box] (A) at (0,0) {A};
    \foreach \pos in {left,right,above,below} {
        \node[\pos=1 of A,matrix] (B-\pos) {\pic{colmat={m=\clst}};\\};
    }

    \node[left=6 of A,box] (C) at (0,0) {C};
    \foreach \pos in {left,right,above,below} {
        \node[\pos=1 of C,box] (D) {D};
    }
    \end{tikzpicture}
\end{document}

Like this?

Just change right=1 of A to right=0 of A, i.e.:

\pic[right=0 of A] (B) {mypic={m=\clst}};

Another possibility is in tikzpicture options (or in tikzset) define

node distance=0cm

and then write

\pic[right=of A] (B) {mypic={m=\clst}};

Updated:

With the drawing code

\foreach \row [count=\j] in \m {
  \foreach \r/\g/\b [count=\i] in \row {
    \fill[fill={rgb,255:red,\r; green,\g; blue,\b}]
      (\i * \w, \j * \w) rectangle ++(\w,\w);
  }
}

• every filled square has its south west corner at (\i*\w, \j*\w) and north east corner at (\i*\w + \w, \j*\w + \w).
• For \i ranging from 1 to \mydimi and j ranging from 1 to \mydimj (inclusive), the constructed bigger rectangle has its south west corner at (1*\w, 1*\w) and north east corner at (\mydimi*\w + \w, \mydimj*\w + \w).
• Hence the center of that bigger rectangle is at (.5*\mydimi*\w + \w, 0.*\mydimj*\w + \w). To put that center at the origin (0, 0), we shift the coordinate by using

shift={(-0.5*\mydimi*\w - \w, -0.5*\mydimj*\w - \w)}

A full example, note that I have slightly simplified the pic definition.

\documentclass[tikz,border=2mm]{standalone}
\usetikzlibrary{positioning}

\makeatletter
\tikzset{
  % colmat
  pics/colmat/.style={code={
    \tikzset{colmat/#1}
    \foreach \row [count=\j] in \pic@colmat@m {
      \xdef\mydimj{\j}
      \foreach \r/\g/\b [count=\i] in \row {\xdef\mydimi{\i}}
    }
    \edef\w{2}%
    \foreach \row [count=\j] in \pic@colmat@m {
      \foreach \r/\g/\b [count=\i] in \row {
        \fill[fill={rgb,255:red,\r; green,\g; blue,\b},
         shift={(-0.5*\mydimi*\w - \w, -0.5*\mydimj*\w - \w)}]
          (\i * \w, \j * \w) rectangle ++(\w,\w);
      }%foreach
    }%foreach
  }},
  colmat/m/.estore in=\pic@colmat@m,
  colmat/m/.initial={{255/0/0}}
}
\makeatother

\begin{document}
\begin{tikzpicture}
  \tikzset{
    box/.style={draw,minimum width=1cm,minimum height=1cm}
  }
  \def\clst{
    {200/10/10},
    {10/10/200},
    {10/200/200}%
  }
  \node[box] (A) at (0,0) {A};
  \foreach \pos in {left,right,above,below} {
    \pic[\pos=2 of A] (B-\pos) {colmat={m=\clst}};
  }

  \node[left=6 of A,box] (C) at (0,0) {C};
  \foreach \pos in {left,right,above,below} {
    \node[\pos=1 of C,box] (D-\pos) {D};
  }
\end{tikzpicture}
\end{document}

Old answer:

Unlike node, a pic has a fixed anchor. That anchor is the (0, 0) inside its drawing commands. See pgf manual, sec. 18.2, paragraph The location of a pic.

In your pic definition, (0, 0) is at the south west corner of filled square. Hence tikz puts every south west corner of pic mypic to positions like left=1 of A.

Inside the definition of pic, moving (0, 0) to the center of filled square solves your problem. Here I use a shift option to offset. It is better to adjust the coordinates used in drawing commands of mypic, to keep its center at origin.

% before
\fill[fill={...},                   ] (\i-1,\j-1) rectangle ++(1,1);
% after
\fill[fill={...}, shift={(-.5, -.5)}] (\i-1,\j-1) rectangle ++(1,1);
% for updated example in question, a shift of (0, -3) is required.