I solved the problem by adding new build configuration that was copied from Debug. I named it DebugNoLargeLib. So I can exclude reference with the following code because $(Configuration) property will be parsed correctly:
<ItemGroup>
<Reference Include="SomeLargeLib.dll" Condition=" '$(Configuration)' != 'DebugNoLargeLib' " />
</ItemGroup>
After I added preprocessor directive NO_LARGE_LIB to the Compiler section for configuration DebugNoLargeLib.
So now I'm able to link without large library and exclude code depending on it from compilation.
But I think this is mistake from Xamarin side that project files processing is not fully supported according to Microsoft specs.