Software Deployment

I would like to know how harmfull it is not to capture a dotnet application with Wise Package Studio 7 as a dotnet application.

The official way to handle dotnet applications is described here:
http://www.symantec.com/connect/articles/handling-gac-assemblies-using-wise-package-studio-70

But if you capture dotnet related files and registry keys as is, does this really have any disadvantages ?

I can imagine that one can have problems with dotnet security configurations but I cannot see any other problems.