My solution was this: I put the import in csproj for the Ilmerge targets file, which:
<Project
DefaultTargets="Build"
xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Import Project="$(MSBuildBinPath)\Microsoft.CSharp.targets" />
<Target Name="AfterBuild">
<CreateItem Include="@(ReferencePath)" Condition="'%(CopyLocal)'=='true'">
<Output TaskParameter="Include" ItemName="IlmergeAssemblies"/>
</CreateItem>
<Message Text="MERGING: @(IlmergeAssemblies->'%(Filename)')" Importance="High" />
<Exec Command=""$(ProgramFiles)\Microsoft\Ilmerge\Ilmerge.exe" /out:@(MainAssembly) "@(IntermediateAssembly)" @(IlmergeAssemblies->'"%(FullPath)"', ' ') /log:ILMerge.log" />
</Target>
<Target Name="_CopyFilesMarkedCopyLocal"/>
</Project>
exe , .
, , , postbuild ( ilmerge), setup exe.