From reading your question it is not clear what you are asking, but I think you want the entire Dock panel to have a 5% margin?
All the new *LayoutPanels in Gwt 2.0 use css absolute positioning, which is why you are seeing the top/left/right/bottom styles. That is why you're strategy for margin:auto doesn't work.
The DockLayoutPanel is really just for layout. I would suggest adjusting the margins of the widgets that you put inside the DockLayoutPanel to achieve the effect you want.
I took a shot at this myself, and I came close to an answer but it is not perfect. I put Labels into each of the DockPanels with a margin of 10px, but the right and bottom borders do not show that margin.
<!DOCTYPE ui:UiBinder SYSTEM "http://dl.google.com/gwt/DTD/xhtml.ent">
<ui:UiBinder xmlns:ui="urn:ui:com.google.gwt.uibinder"
xmlns:g="urn:import:com.google.gwt.user.client.ui">
<ui:style>.label {
background: #666;
color: #fff;
font-size: 14pt;
padding: 5px;
margin: 10px;
height: 100%;
width: 100%;
}</ui:style>
<g:DockLayoutPanel unit='PCT'>
<g:north size='10'>
<g:Label addStyleNames="{style.label}">Top</g:Label>
</g:north>
<g:center>
<g:Label addStyleNames="{style.label}">Body</g:Label>
</g:center>
<g:west size='10'>
<g:Label addStyleNames="{style.label}">West</g:Label>
</g:west>
<g:south size="10">
<g:Label addStyleNames="{style.label}">South</g:Label>
</g:south>
</g:DockLayoutPanel>