You can use XmlMassUpdate instead of the XmlUpdate task.
<ProjectExtensions>
<defaultProxy>
<proxy usesystemdefault="False" proxyaddress="http://IPADDRESS:PORT"/>
</defaultProxy>
</ProjectExtensions>
<Target Name="SubstituteFromWebConfig">
<XmlMassUpdate
NamespaceDefinitions="msb=http://schemas.microsoft.com/developer/msbuild/2003;n=http://schemas.microsoft.com/.NetConfiguration/v2.0"
ContentFile="$(BuildDir)\Builds\_PublishedWebsites\Presentation\Web.config"
ContentRoot="/n:configuration/n:system.net"
SubstitutionsFile="$(MSBuildProjectFullPath)"
SubstitutionsRoot="/msb:Project/msb:ProjectExtensions/msb:system.web" />
</Target>
node, ContentRoot ContentFile, , SubstitutionsRoot SubstitutionsFile ( MSBuild).
MSBuild ProjectExtensions, XML , MSBuild. > .
( XmlMassUpdate, XmlRead node ProjectExtensions XmlUpdate.)