stroke width causes values to go over the zero line

I have made a bar chart which have two columns per category. These columns can have positive or negative values. My data values would sometimes have extremely large and small range or gap which results to small values not being visible enough. I have added a strokeWidth that extremely small values will have a minimum pixel and would still be visible in the graph.

After adding the strokeWidth, it messes with the columns axis starting position from the zero line. Negative items now displays above the zero line when it should be starting from there.

I think it is related to this: https://github.com/vega/vega/pull/3487

Try setting an offset on your y2:

{
  "$schema": "https://vega.github.io/schema/vega/v5.json",
  "width": 700,
  "height": 370,
  "autosize": {"type": "fit", "contains": "padding"},
  "padding": {"bottom": 2, "right": 9, "left": 5},
  "config": {
    "axis": {
      "labelFont": "HelveticaNeueLTW01-55Roman",
      "titleFont": "HelveticaNeueLTW01-55Roman"
    }
  },
  "data": [
    {
      "name": "capital_flows",
      "values": [
        {"label": "2012", "capital_inflow": 208.91, "capital_outflow": -500},
        {"label": "2013", "capital_inflow": 115.61, "capital_outflow": -458.76},
        {"label": "2014", "capital_inflow": 135.7, "capital_outflow": -335.23},
        {"label": "2015", "capital_inflow": 148.75, "capital_outflow": -83.61},
        {"label": "2016", "capital_inflow": 152.57, "capital_outflow": 0.36},
        {"label": "2017", "capital_inflow": 198.23, "capital_outflow": 0.29},
        {"label": "2018", "capital_inflow": 911.81, "capital_outflow": 0.58},
        {"label": "2019", "capital_inflow": 5342.44, "capital_outflow": 14.48},
        {"label": "2020", "capital_inflow": 4664.46, "capital_outflow": 11.51},
        {"label": "2021", "capital_inflow": 3800.92, "capital_outflow": 7.54},
        {"label": "2022", "capital_inflow": 6633, "capital_outflow": 12.04},
        {"label": "2023", "capital_inflow": 7381.93, "capital_outflow": 5.31},
        {"label": "2024", "capital_inflow": 3612.31, "capital_outflow": 3.7}
      ],
      "transform": [
        {"type": "formula", "expr": "split(datum.label, ' ')", "as": "label"}
      ]
    },
    {
      "name": "parsed",
      "source": ["capital_flows"],
      "transform": [
        {
          "type": "aggregate",
          "fields": [
            "capital_inflow",
            "capital_inflow",
            "capital_outflow",
            "capital_outflow"
          ],
          "ops": ["min", "max", "min", "max"],
          "as": ["min_value1", "max_value1", "min_value2", "max_value2"]
        },
        {
          "type": "formula",
          "expr": "datum.max_value1 == 0 && datum.max_value2 == 0 ? 1 : datum.max_value1 > datum.max_value2 ? abs(datum.max_value1) : abs(datum.max_value2)",
          "as": "mergedMax"
        },
        {
          "type": "formula",
          "expr": "datum.min_value1 == 0 && datum.min_value2 == 0 ? -1 : datum.min_value1 < datum.min_value2 ? abs(datum.min_value1) : abs(datum.min_value2)",
          "as": "mergedMin"
        },
        {
          "type": "formula",
          "expr": "datum.mergedMax > datum.mergedMin ? datum.mergedMax : datum.mergedMin",
          "as": "max"
        },
        {"type": "formula", "expr": "-(datum.max)", "as": "min"}
      ]
    }
  ],
  "scales": [
    {
      "name": "x",
      "type": "band",
      "range": "width",
      "domain": {"data": "capital_flows", "field": "label"}
    },
    {
      "name": "y",
      "type": "linear",
      "range": "height",
      "nice": true,
      "zero": false,
      "domain": {"data": "parsed", "field": "limit"},
      "domainMin": {"signal": "pluck(data('parsed'), 'min')"},
      "domainMax": {"signal": "pluck(data('parsed'), 'max')"}
    }
  ],
  "axes": [
    {
      "orient": "bottom",
      "scale": "x",
      "zindex": 1,
      "labelFontSize": 12,
      "labelColor": "#85868C",
      "labelAlign": "center",
      "labelLineHeight": 16.8,
      "labelFontWeight": "normal",
      "labelPadding": 8,
      "labelOpacity": 1,
      "domain": false,
      "domainColor": "#e5e5e5",
      "domainWidth": 1,
      "ticks": false
    },
    {
      "orient": "left",
      "scale": "y",
      "zindex": 0,
      "labelFontSize": 12,
      "labelColor": "#85868C",
      "labelLineHeight": 16.8,
      "labelFontWeight": "normal",
      "labelPadding": 8,
      "labelOpacity": 1,
      "domain": false,
      "domainColor": "#e5e5e5",
      "grid": true,
      "gridOpacity": 0.5,
      "ticks": false,
      "tickCount": {"signal": "pluck(data('parsed'), 'max') < 1000 ? 4 : 6"},
      "gridDash": {"signal": "datum.value == 0 ? [0,0] : [4,4]"},
      "encode": {
        "labels": {
          "update": {
            "text": {
              "signal": "if(abs(datum.value) >= 1e9, format(datum.value/1e9, '$,.1~f') + 'B', if(abs(datum.value) >= 1e6, format(datum.value/1e6, '$,.1~f') + 'M', if(abs(datum.value) >= 1e3, format(datum.value/1e3, '$,.1~f') + 'K', format(datum.value, '$,.2~f'))))"
            }
          }
        }
      }
    }
  ],
  "marks": [
    {
      "name": "inflow",
      "type": "rect",
      "from": {"data": "capital_flows"},
      "encode": {
        "enter": {
          "xc": {"scale": "x", "field": "label", "band": 0.5},
          "width": {"value": 16},
          "y": {"scale": "y", "field": "capital_inflow"},
          "y2": {"scale": "y", "value": 0},
          "fill": {"value": "#68c487"},
          "cornerRadiusTopLeft": {
            "signal": "datum.capital_inflow > 0 ? '1' : '0'"
          },
          "cornerRadiusTopRight": {
            "signal": "datum.capital_inflow > 0 ? '1' : '0'"
          },
          "cornerRadiusBottomLeft": {
            "signal": "datum.capital_inflow > 0 ? '0' : '1'"
          },
          "cornerRadiusBottomRight": {
            "signal": "datum.capital_inflow > 0 ? '0' : '1'"
          },
          "stroke": {"signal": "datum.capital_inflow !== 0 ? '#68c487': null"}
        }
      }
    },
    {
      "name": "outflow",
      "type": "rect",
      "from": {"data": "capital_flows"},
      "encode": {
        "enter": {
          "xc": {"scale": "x", "field": "label", "band": 0.5, "offset": 19},
          "width": {"value": 16},
          "y": {"scale": "y", "field": "capital_outflow"},
          "y2": {"scale": "y", "value": 0, "offset":1.5},
          "fill": {"value": "#FFB066"},
          "cornerRadiusTopLeft": {
            "signal": "datum.capital_outflow > 0 ? '1' : '0'"
          },
          "cornerRadiusTopRight": {
            "signal": "datum.capital_outflow > 0 ? '1' : '0'"
          },
          "cornerRadiusBottomLeft": {
            "signal": "datum.capital_outflow > 0 ? '0' : '1'"
          },
          "cornerRadiusBottomRight": {
            "signal": "datum.capital_outflow > 0 ? '0' : '1'"
          },
          "stroke": {"signal": "datum.capital_outflow !== 0 ? '#FFB066': null"},
          "strokeWidth": {"value": 1.5}
        }
      }
    }
  ]
}