Had an interesting case today. I believe that what is happening is rem units for different parts of the page rendering use different root elements. The @page margin (@top, @bottom, etc.) appear to be based on the font-size defined on @page, whereas non-margin parts appear to be based on the font-size of the html element. If I drop something like this into the CSS, then suddenly the size of the page @top and the box in the PDF seem to be ~roughly the same size:
html {
font-size: 50%;
}