The modifications DNN has over our controls is the exact reason why we do not support that environment and we cannot provide definitive answers as to how our controls are used there. It is best if you address such queries to the DNN support and/or forums.
What I can suggest as a possible option is to add a bindingRedirect element for the new version, but this is likely to break the existing DNN functionality since the custom classes and wrappers will not be available any longer in the vanilla dlls we provide.
You cannot have two versions of the same assembly (Telerik.Web.UI.dll and Telerik.Web.UI.Skins.dll in this case) used in the same project. This is a generic .NET limitation.
As for commercial use - I have forwarded your query to our sales team and they will follow up with you on this matter.
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