Because spacing is set to 6mm in the horizontal direction, there's 6mm on either side of column 2 even though that column has width zero.

You could remove the empty column and have edges with fractional coordinates, like this:

#context diagram(
  debug: true,
  spacing: (6mm, 0mm),
  node-stroke: 1pt,
  {
    let data = fletcher.shapes.parallelogram.with(angle: 30deg)

    let c = [Ground-Truth Image, $I_G$]
    let s = measure(c)
    let w = s.width   6pt * 2

    node((0, 0), [Input Image, $I$], shape: data, width: w)
    node((0, 2), c, shape: data)

    node((1, 0), [Base network, $F_L$])
    node((1, 2), [Base network, $F_L$])

    node((2, 1), [MSE])

    node((3, 1), [Result, $S$], shape: data)

    edge((0, 0), "r", "-|>")
    edge((0, 2), "r", "-|>")

    edge((1, 0), (rel: (.66,0)), "d", (2,1), "-|>")
    edge((1, 2), (rel: (.66,0)), "u", (2,1), "-|>")

    edge((2, 1), "r", "-|>")
  }

(or maybe this is better style for this case?)

You could remove the empty column and have edges with fractional coordinates, like this:

Right, I guess that works. I wanted to keep the vertical edge exactly in the middle between the nodes, is that still possible here without eyeballing the fraction?

(or maybe this is better style for this case?)

Indeed, maybe this style is better here. However, it has a bit of an inverse problem: I feel like now I want to ever so slightly reduce the spacing between "Base network" and "MSE" on this example, since the top and bottom arrows make it look a bit wider.

is that still possible here without eyeballing the fraction?

Hmm. I can't come up with an automatic way with the current features. It would be great if it were possible to use cetz anchors like "east" to refer to the edges of the nodes, because then you could use something like ("node1.east", 50%, "node2.west") to get the exact middle. Unfortunately cetz anchors aren't supported yet in fletcher.

Even without that, though, it might be good to allow grid spacings to be individually controlled. I'll make this a feature request. Any thoughts on how you'd want the syntax to be?

Any thoughts on how you'd want the syntax to be?

I was thinking, maybe similar to built-in Typst grid and table row-gutter/column-gutter? Where you can pass one number to set all, or pass an array of numbers to set each one individually. Or even like align where you can also pass a function that takes the X, Y position and returns the value.