Don't take this as Esoteric's official word.
But the truth is that it's still best to whitespace-strip the images BEFORE packing, and not after. Having huge images in Spine editor also slows down the editor and causes really inconvenient behavior when selecting and viewing things. It'll be a bit of a pain to do but one thing you can do right now is re-export those individual images and realign them in the setup pose. The hard part is re-doing the meshes. I don't know if that'll be doable on your end.
But note, supporting real whitespace stripping for meshes isn't something any graphics package can do right now for all situations. I wonder if it'll ever be possible.
@Shiu/Nate
I still say Spine Editor should show a clear warning when it detects that you're using images that haven't been whitespace-stripped.
Another feature might be whitespace stripping and whitespace adding (nondestructive or otherwise) within the editor, but before packing. The whitespace-adding is only for those MeshAttachments that you want to give a little extra whitespace to so you can have nicer mesh intead of one that breaks 'cause you have to hug the sides of the rectangle.