The fact that the ScriptReferences are added to the RadScriptManager when you initially create a Telerik website/page or application is intended behavior. Please take a look at the following help article for more detailed information on why you need to use the RadScriptManager:
Considering the jQuery intellisense you should be able to use it no matter if you have a master/content scenario or a simple web page. As long as you have registered the scripts correctly (as explained here
and in the article that you pointed out) there should not be any issue with the intellisense (see the attached images).
the Telerik team
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