It's because <svg> is an inline element - setting it to display: block; will remove those effects e.g. caused from a line-height.
svg {
display: block;
}
<!DOCTYPE html>
<html>
<body>
<div align="center" style="width:100%; height:100%; padding: 0px; margin: 0px;">
<svg height="500" version="1.1" width="1000" xmlns="http://www.w3.org/2000/svg" id="raphael-paper-0" style="overflow: hidden; -webkit-tap-highlight-color: rgba(0, 0, 0, 0); -webkit-user-select: none; cursor: default; position: relative; background-color: rgb(255, 255, 255);">
<circle cx="500" cy="250" r="100" stroke="green" stroke-width="4" fill="yellow" />
</svg>
</div>
</body>
</html>
