Well, one main difference in PE Header between Win32 and .NET assemblies (.exe files), is the COM Directory and some metadata fields.Only .Net assemblies need the COM Directory.Why for?That's the way .Net Runtime recognizes this assembly as managed code.If it's a C++ with managed .Net extensions, only the extensions used are managed code..The rest of the file is pure Win32, so the COM Directory is null.Before loading MSCORWKS.DLL it MUST load MSCOREE.DLL.
Note that MSCOREE is the main runtime dll of the framework(s) even if multiple versions are installed.

Unfortunately i haven't look at it yet to have a better view of the protector..