Is there anyway to create a BizTalk map with multiple input schema "from scratch" ?
i.e. not creating an orchestration and a transform shape and selecting multiple messages in the Source
No, there isn't a way to create a multi-schema input map in Visual Studio for either BizTalk 2006, 2009 or 2013 (thanks for the clarification @Krishan) without going via the Orchestration/Transform shape route. The only other option is to manually write a map by hand in a text editor, or from a template.
Bear in mind that with the Orchestration/Transform solution, you can throw the Orchestration away once you've used it to create the map.