That's not a problem. You can switch between attachments of different sizes if you need armor or weapon parts that are bigger or smaller. You just need to make sure you resize by adding an equal number of pixels to all four sides and it will keep the pivot. You can also resize it any way you want import them in Spine to find out the correct pivot/offset to use.
Are you using Spine Essential?
I seemed to be able to fix the problem pretty easily by trimming the atlases naively but this isn't actually possible if you're using meshes. If you're using meshes, you need to trim them BEFORE you make the meshes.
You should know also though that your animation is doing some other weird thing. (the flickering is happening with the weapons, and this is actually because of the actual animation data.)
I think you didn't want to key the weapon attachments here. If you remove all those keys, the flickering should go away.