I almost figured out how to draw what I want by piecing together two answers here (@Ignasi for TiKZ matrix of objects and @alexraasch for L shaped boxes in tikz matrix).
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{matrix, backgrounds}
\begin{document}
\begin{tikzpicture}[
mycell/.style={draw, minimum size=1cm},
dot1/.style={mycell,
append after command={\pgfextra \fill (\tikzlastnode)
circle[radius=10pt]; \endpgfextra}},
dot2/.style={mycell,
append after command={\pgfextra \fill[white] (\tikzlastnode)
circle[radius=10pt]; \endpgfextra}},
dot3/.style={mycell,
append after command={\pgfextra \draw[thick] (\tikzlastnode)
circle[radius=10pt]; \endpgfextra}}, ]
\matrix (m) [matrix of nodes, row sep=-\pgflinewidth, column sep=-\pgflinewidth,
nodes={mycell}, nodes in empty cells]
{
|[dot2]|&&&|[dot1]|&&\\
&&&&&\\
&&&&|[dot1]|&\\
|[dot1]|&&&&&\\
&&&&&\\
&|[dot3]|&&&&\\
};
\begin{scope}[on background layer]
\path [fill=black!10]
(m-1-1.north west) -- (m-2-1.south west)
-- (m-2-2.south east) -- (m-3-2.south east)
-- (m-3-5.south east) -- (m-2-5.north east)
-- (m-2-3.north east) -- (m-1-3.north east)
-- cycle;
\draw (m-1-1.north west) -- (m-2-1.south west)
-- (m-2-2.south east) -- (m-3-2.south east)
-- (m-3-5.south east) -- (m-2-5.north east)
-- (m-2-3.north east) -- (m-1-3.north east)
-- cycle;
\end{scope}
\end{tikzpicture}
\end{document}
creates
I want the white disc in the m-1-1 position (a dot2) to have a black boundary as in m-6-2 (a dot3). My naive efforts of combining \draw and \fill didn't work. I'm open to entirely different solutions if what I want is tricky with the code I spliced together.

