In Spine 3.6 you can export from Photoshop with the script, import into your project under a new skeleton, then (starting in 3.6) you can drag bones, slots, and attachments from one skeleton to another. This allows you to move your perfectly positioned attachments from the newly imported skeleton to your existing skeleton, then you can delete the imported skeleton.
Another way to do it is to create a skeleton where each image is large enough (using whitespace around the edges) for all the different attachments you will place there. This way all your images will be the same size and Shiu's method will work for you. However, the real advantage to this method is that you don't have to bring the attachments into Spine at all, you could generate the attachments at runtime. This can be helpful when you may have hundreds or thousands of attachment images.
