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I found a resolution in the end. The problem was that the Chart itself was being scaled correctly to match the DPR of the device, but the axis being animated was not.
Scaling the axis myself resolved the problem โ https://jsfiddle.net/EmmaLouise/eb1aqpx8/3/:
var scale = window.devicePixelRatio;
var sourceCanvas = chartTest.chart.canvas;
var copyWidth = chartTest.scales['y-axis-0'].width - 10;
var copyHeight = chartTest.scales['y-axis-0'].height + chartTest.scales['y-axis-0'].top + 10;
var targetCtx = document.getElementById("axis-Test").getContext("2d");
targetCtx.scale(scale, scale);
targetCtx.canvas.width = copyWidth * scale;
targetCtx.canvas.height = copyHeight * scale;
targetCtx.canvas.style.width = `${copyWidth}px`;
targetCtx.canvas.style.height = `${copyHeight}px`;
targetCtx.drawImage(sourceCanvas, 0, 0, copyWidth * scale, copyHeight * scale, 0, 0, copyWidth * scale, copyHeight * scale);
var sourceCtx = sourceCanvas.getContext('2d');
// Normalize coordinate system to use css pixels.
sourceCtx.clearRect(0, 0, copyWidth * scale, copyHeight * scale);
rectangleSet = true;
Source:stackexchange.com