Thank you for contacting us.
First let me clarify that Silverlight assemblies can't be register neither in the GAC nor in the .net tab. The reason is that they target the Silverlight runtime not the .net runtime. Silverlight assemblies can be registered under the Silverlight tab and in fact when you use the msi installation package they are registered there. If you don't use the msi installation package then you should register them manually.
The reason why the Upgrade Wizard doesn't register the assemblies is limitation in the Silverlight support in Visual Studio.
I hope the information provided answers your questions. If any future inquires arise don't hesitate to contact us again.
the Telerik team