Thank you for your code and an explanation.

Let's assume that the last MPpage was a \startuseMPgraphic{boxes} .... \stopuseMPgraphic. Suppose I wanted to use these pictures in a presentation. On the first slide, I can use

\useMPgraphic[stacking=0]{boxes}

to show the three boxes, and on the next slide, I can use

\useMPgraphic[stacking={-1,0}]{boxes}

I tried to reproduce your example using \startuseMPgraphic{boxes} … \stopuseMPgraphic, and useMPgraphic[stacking=0]{boxes} .

\startMPdefinitions
  input boxes;

  primarydef a +- b =
    a -- (xpart a, ypart b) -- b
  enddef ;
  primarydef a -+ b =
    a -- (xpart b, ypart a) -- b
  enddef ;
\stopMPdefinitions
\defineframed
  [boxframed]
  [
    width=6em,
    height=2\lineheight,
    align={middle,lohi},
    background=color,
    backgroundcolor=blue,
    foregroundcolor=white,
    forefroundstyle=bold,
  ]

\startuseMPgraphic[offset=2mm]{boxes}
  boxit.A("\boxframed{Box A}");
  boxit.B("\boxframed{Box B}");
  boxit.C("\boxframed{Box C}");

  defaultdx := 0pt;
  defaultdy := 0pt;

  A.c = origin;

  B.w - A.e = (1cm, 0);

  0.5[ A.s, B.s ] - C.n = (0, 1cm);

  stacking := 0;
  drawunboxed(A,B,C);
  stacking := 1;
  drawarrow A.s +- C.w ;
  drawarrow B.s +- C.e ;

  newpath highlight;

  highlight := (A.sw -- B.se -- B.ne -- A.nw) enlarged EmWidth;
  fill highlight withcolor "darkgray" withstacking -1;

\stopuseMPgraphic

\starttext
\useMPgraphic[stacking={0}]{boxes}
\useMPgraphic[stacking={0,1}]{boxes}
\useMPgraphic[stacking=-1]{boxes}
\stoptext