In reply to your first question.
I don't think you are using InstallShield Tuner to create a MST file. Based on your description you are using InstallShield Developer. When you add an external file into the MST file from InstallShield Developer it presents you with an "Select Media Location" dialog and "Stream the new CAB file into the Windows Installer package" option is grayed out.
The reason why this option is grayed out is becuase we don't want to modify the original MSI package. The whole idea of transform files is to save the changes you make to the MSI package. This way your original MSI package is not modified. At run time you will apply the transform with the original MSI package and Windows Installer engine will take care of merging the contents of both the transform and MSI package.
As far as streaming the cab file into transform is concerned I don't think it is possible. You can also use InstallShield Tuner to do the same thing and Tuner will by default save the changes into the cab file without presenting you with this dialog.
Now to your question #2
InstallShield Tuner has a check box that says "Response Transform". This check box is located just above the "Create" button in "Create a new transform" view. If you check this check box and then click on "Create" button you will be able to create a response transform.
Now to your final question
Take a look at the Shortcut table in MSI help. What is displayed in the shortcut view in Tuner or Developer is ultimately mapped to the Shortcut table in MSI package. You can also check this URL for information on the Shortcut table.
http://msdn.microsoft.com/library/default.asp?url=/library/en-us/msi/setup/shortcut_table.asp