qwer As you said, you cannot set the mesh hull beyond the boundaries of the original image. Therefore, in a case like the one you mentioned, you should set more padding when exporting the images using scripts, or use layer masks to match the size of the image (though this is only available in PhotoshopToSpine).
The reason for this restriction can only be answered by Nate, but my personal guess is that allowing vertex placement without regard to image boundaries would make the texture packing process too complicated.
For your information, even if the images used in your skeleton have a lot of whitespace, you can remove it when packing the texture if you enable
Strip whitespace X/Y in the Texture Packer settings. This will ensure that the extra whitespace will not be a problem in the final packed texture atlas. Therefore, it is a good idea to keep the image with a sufficient amount of padding when you export it from the image editor, to allow for more freedom in the positioning of the mesh vertices.