The tool used by CF to setup the websites in IIS will only do it at top level. So the Default Web Site, it wont apply to folders below it. This is because it makes changes to the ISAPI filters which can only be changed on the website level not subfolders.
You would have to setup different websites for each app for this to work.
Yes, but it was also possible to change the File Handler per subfolder, so I can imagine, that I change the extension handler settings for .cfc and .cfm from D:\ColdFusion9\config\wsconfig\1\isapi_redirect.dll changing to D:\ColdFusion11\config\wsconfig\1\isapi_redirect.dll
You could try it, but the top level ISAPI filter will still be using CF9's dll, which means there will be a conflict, and most likely causes errors.