I checked now with BizTalk 2013 project in Visual Studio 2012 and when I install my log4net.Ext.Serializable package into .btproj project - it works. NuGet adds this to .btproj file:
<Reference Include="log4net, Version=1.2.15.0, Culture=neutral, PublicKeyToken=669e0ddf0bb1aa2a, processorArchitecture=MSIL">
<HintPath>..\packages\log4net.2.0.5\lib\net45-full\log4net.dll</HintPath>
<Private>True</Private>
</Reference>
<Reference Include="log4net.Ext.Serializable, Version=1.0.0.2, Culture=neutral, PublicKeyToken=02e779351b902449, processorArchitecture=MSIL">
<HintPath>..\packages\log4net.Ext.Serializable.1.0.0\lib\net20\log4net.Ext.Serializable.dll</HintPath>
<Private>True</Private>
</Reference>
I have NuGet version:NuGet Package Manager 2.8.60318.667