As far as I can tell, they just align in the central-most sides of each .png.
There is an issue where parts of a gun sometimes appear to be slightly separated. It could be related to that (if it is, there is no fix).
I wish I could be more helpful. :/
So the problem is probably just the sprites being designed for different size guns. You could just manually edit them to line up properly.
or make custom sprites. The best thing to do is to make sure the top or bottom pixel on the end(s) is always in the same spot in relation to the top/bottom of the .png.
Or atleast close enough to it that things will connect together decently.
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