Why don't you use .NET 4 or better yet .NET 4.5?
Web.config is not capable of modifying itself, maybe the runtime or IIS could be doing that but it never happens to me and I have no idea why it would need those. Maybe if you installed .NET 2 on your win 8 dev machine it needs to add those because they are so old but the deployment server running an older OS doesn't need them.
.NET 3.5 is a superset of 2.0 but still those assemblies don't generally need to be listed in web.config.
I assume you are using .NET 3.5 because for sure .NET 4 would not add those assemblies.
My recommendation to everyone is stop using .NET 3.5 and migrate to 4.5 and using the 4.0 package of mojoPortal. We may drop support for .NET 3.5 in the not too distant future, it is time for .NET 3.5 to be retired. Time and progress march on.