Question about packaging dotnet applications

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:

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.

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