for (el of chart.children) {
i++
previous__element = chart.children[i - 1]
if (el.classList.contains('rule')) {
//pass
} else {
line = el.children[0].children[0]
pos1 = previous__element.children[2].getBoundingClientRect()
position1 = {
top: pos1.top,
left: pos1.left,
}
pos2 = el.children[2].getBoundingClientRect()
console.log(previous__element.children[2])
console.log(el.children[2])
position2 = {
top: pos2.top,
left: pos2.left,
}
line.setAttribute('x1', Math.trunc(pos1.left))
line.setAttribute('y1', Math.trunc(pos1.top))
line.setAttribute('x2', Math.trunc(pos1.left))
line.setAttribute('y2', Math.trunc(pos1.top))
line.setAttribute('stroke', 'white')
}
}
html that gets output:

For some reason this does not actually show the lines, when hovering over them in dev tools it shows the height and width is 0. I'm trying to get the line to connect to the markers in the elements.
In this example I use position relative/absolute on all the elements. I don't know if that fits your solution, but the core of the example is that the SVG document is in the background of all the boxes. So, all the lines could be placed in that one SVG document.
Maybe the reason why your lines are not showing up is that they mis the stroke-width or that your SVG element does not have a width and a height.
let chart = document.querySelector('#chart');
let poschart = chart.getBoundingClientRect();
let line = chart.querySelector('svg line');
let boxs = chart.querySelectorAll('div.box');
let pos1 = boxs[0].getBoundingClientRect();
line.setAttribute('x1', pos1.x+pos1.width/2-poschart.x);
line.setAttribute('y1', pos1.y+pos1.height/2-poschart.y);
let pos2 = boxs[1].getBoundingClientRect();
line.setAttribute('x2', pos2.x+pos2.width/2-poschart.x);
line.setAttribute('y2', pos2.y+pos2.height/2-poschart.y);
#chart {
position: relative;
width: 400px;
height: 300px;
margin: 10px 20px;
border: thin solid black;
}
#chart svg {
position: absolute;
}
.box {
position: absolute;
padding: .5em;
border: thin solid black;
background-color: white;
}
<div id="chart">
<svg viewBox="0 0 400 300" width="100%" height="100%">
<line stroke="black" stroke-width="2"/>
</svg>
<div class="box" style="left:50px;top:180px">Box 1</div>
<div class="box" style="left:310px;top:100px">Box 2</div>
</div>