Yes, it is possible
to make portable that is not installed into Program Files folder. But it will not be easy as JPE Quickie or JPE Setup Capture.
In order to do that, use The 12 Step Program
method. When you come to the step of editing configuration ini, add the non-special folder path in the [FilesystemInclude] and [SpecialFolders] so that JPE recogize the files install into that folder. For example
JauntePE the portable maker: <<JauntePE Google Site