Updated on 20/02/2013
As @A-student pointed out in the comments, my previous solution would force you to add the MSBuild stuff in each and every project in a solution.
This one only requires you enter it on the projects that actually have a XAP/APPX file output:
<PropertyGroup>
<FilesToXapDependsOn>$(FilesToXapDependsOn);AfterFilesToXapDependsOn</FilesToXapDependsOn>
</PropertyGroup>
<Target Name="AfterFilesToXapDependsOn">
<ItemGroup>
<FilteredPackagingOutputs Remove="@(FilteredPackagingOutputs)" Condition="'%(FilteredPackagingOutputs.OutputGroup)' == 'CopyLocalFilesOutputGroup' AND '%(FilteredPackagingOutputs.Extension)' == '.xml'" />
</ItemGroup>
</Target>
It's a bit of a hack and should be used carefully (not sure right now of what implications this might actually have), but seems to do the job perfectly for now!