Not sure if this might help or not. I am a Gimp user and not a PS user but searching online I found something that might help with PS seeing as that's the same thing that Gimp does. When exporting your layers as png, make sure "trim layers" is ticked off. What this does (like the name suggests) is keeps the images at their sizes without removing the transparent background. Yes the files will be a bit bigger but it will be manageable, and their size becomes irrelevant when you attach bones to them. In Spine, place your images just like normal the only difference is after you are done, you will have to change the origin of each image (origin of an image is located next to the move tool at the bottom left). Since the transparent sections aren't trimmed off, all the images will fit perfectly in place if they have the same origin. I know it sounds like lot of work but trust me, changing the origins are less time consuming than making everything fit perfectly. And don't worry, if you export the Spine file, Spine will delete the extra transparent areas.

Hope this helps.

It seems as untrimming isn't the best choice for the sake of your game performance as it "kills your GPU" according to this post Texture UVs assigned incorrectly on some body parts

Remember how whitespace stripping doesn't play nice with meshes? That still applies. Texture Packing - Spine User Guide

If you or your artist/animator is working on any other skeletons, I recommend you immediately trim all your parts images and realign your images your before continuing any work.

Unity_2016-08-18_12-50-32.png

Your images should be trimmed. Not like this. This will kill your GPU.

It may be the longer way but it's also the safest so far, one thing you could do is export everything together as a skeleton, align it with your moved root and take note of how much it has been moved, (I usually create a bone that I later delete for this task), then take note of where the added images are and align them properly (since you can't transfer the newly aligned images from one skeleton to the other as far as I know) and then place and align the images accordingly.
It's not really pleasant but at least you're sure they're performative and they're well placed.
Anyways I hope there's a better way so I'm here to listen to suggestions as well if someone comes up with better ideas (:

Interesting. If that's the case then I guess you might be out of luck with that shortcut....but I however remember a trick someone used. You can simply import a full image of your character and lock it in as a background (by checking the background button). When checked, the image is kept from being moved so you can just place the part onto it to build it. That should make things easier.