pgfplots: Best way to draw a "patchwork" diagram

Here is a very basic option. Use pgfplotstable and plain TikZ to convert the data in a plot. Since it is very basic, it may be easy to customize. The prize that you have to pay is that you need to fix some things by hand in

x=3mm,y=3mm,declare function={nrows=3;}

which sets the units and the number of rows. (In all fairness, also in some pgfplots scenarios you have to set the number of rows or columns explicitly.)

documentclass[tikz,border=3mm]{standalone}
usepackage{pgfplotstable}
begin{document}
begin{tikzpicture}[x=3mm,y=3mm,declare function={nrows=3;}]
pgfplotstableread{%
x    y    color    label
% First Column
10   5    green    Labelx1y1
10   15   green    Labelx1y2
10   20   green    Labelx1y3
% Second Column
18   5    green    Labelx2y1
18   15   green    Labelx2y2
18   20   green    Labelx2y3
% Third Column
25   5    green    Labelx3y1
25   15   green    Labelx3y2
25   20   red      Labelx3y3
}dataA
pgfplotstablegetrowsof{dataA}%
pgfmathtruncatemacro{numrows}{pgfplotsretval-1}%
edeflastx{0}%
edeflasty{0}%
pgfplotsforeachungroupedX in{0,...,numrows} {%
pgfplotstablegetelem{X}{x}ofdataA
letxpgfplotsretval
pgfplotstablegetelem{X}{y}ofdataA
letypgfplotsretval
pgfplotstablegetelem{X}{color}ofdataA
letmycolorpgfplotsretval
pgfplotstablegetelem{X}{label}ofdataA
letmylabelpgfplotsretval
draw[fill=mycolor] (lastx,lasty) rectangle (x,y) node[midway]{mylabel};
letlastyy
pgfmathtruncatemacro{itest}{Mod(X+nrows+1,nrows)}%
ifnumitest=0relax
edeflasty{0}%
letlastxx
fi
}
end{tikzpicture}
end{document}

One can actually embed this into pgfplots. There is a small issue regarding the expansion, hence the edef and noexpand trickery (see the discussion on p. 545 of the pgfplots manual v1.17).

documentclass[tikz,border=3mm]{standalone}
usepackage{pgfplotstable}
usepackage{pgfplots}
pgfplotsset{compat=1.17}
begin{document}
begin{tikzpicture}[declare function={nrows=3;}]
begin{axis}[width=12cm,title=Random title]
pgfplotstableread{%
x    y    color    label
% First Column
10   5    green    Labelx1y1
10   15   green    Labelx1y2
10   20   green    Labelx1y3
% Second Column
18   5    green    Labelx2y1
18   15   green    Labelx2y2
18   20   green    Labelx2y3
% Third Column
25   5    green    Labelx3y1
25   15   green    Labelx3y2
25   20   red      Labelx3y3
}dataA
pgfplotstablegetrowsof{dataA}%
pgfmathtruncatemacro{numrows}{pgfplotsretval-1}%
edeflastx{0}%
edeflasty{0}%
pgfplotsforeachungroupedX in{0,...,numrows} {%
pgfplotstablegetelem{X}{x}ofdataA
letxpgfplotsretval
pgfplotstablegetelem{X}{y}ofdataA
letypgfplotsretval
pgfplotstablegetelem{X}{color}ofdataA
letmycolorpgfplotsretval
pgfplotstablegetelem{X}{label}ofdataA
letmylabelpgfplotsretval
edeftemp{noexpandaddplot[fill=mycolor] coordinates {(lastx,lasty) (lastx,y)
(x,y) (x,lasty) (lastx,lasty)};
noexpandpath (lastx,lasty) rectangle (x,y) node[midway]{mylabel};}
temp
letlastyy
pgfmathtruncatemacro{itest}{Mod(X+nrows+1,nrows)}%
ifnumitest=0relax
edeflasty{0}%
letlastxx
fi
}
end{axis}
end{tikzpicture}
end{document}