Normally, the page is built as a table with three rows (this is a simplified view):
HTML Code:
<table>
<tr>Header</tr>
<tr>Middle</tr>
<tr>Footer</tr>
</table>
When you set the 'Full Width Header' option to 'Yes' the header area is removed from the table and becomes a <div>…</div> so you have
HTML Code:
<div>Header>
<table>
<tr>Middle</tr>
<tr>Footer</tr>
</table>
and the Header is set to a width of %100. All positioning of elements in the header happens in relation to this <div> and it is not tied to the table containing the middle and footer.
I hope this helps you out.