I cannot reproduce that, converting the following html
Code:
<!DOCTYPE html>
<html>
<head>
<title>t</title>
<meta charset="utf-8" />
</head>
<body>
<div style="margin: 1em auto">centered</div>
</body>
</html>
with
ebook-convert file.html .azw3 --expand-css
results in the following css in the azw3
Code:
.calibre1 {
display: block;
margin-bottom: 1em;
margin-left: auto;
margin-right: auto;
margin-top: 1em
}