My ideal tool for texture atlases is TexturePacker.
I think, if it will be made the same way - it would be great.
Texture packer one of the most popular tool.
Texture Packer save size of trimmed alpha and it used when calculating pivot point. That mean that pivot point calculated in center of original image, and then images are trimmed. but they are still using original image pivot (it can be out of bounds the new trimmed image)
In most case this items can be in different atlases. One with trimmed alpha and other where this option turned off.
All this functions already implemented in texturepacker. I already asked about realisation of supporting atlases from the Texture Packer here and @stormarchitextor ask to support here