Hi, yeah that's just a natural limitation of animation complexity because not every piece is the same size. It's one of those things that can't be covered by a basic generator because there's just too many possibilities. You can edit pieces as needed, either in an image editor for specific characters or in-engine if you're assembling them in your own game that way.
It's mentioned a couple times in the guide, here's a quote from the section on the included premade sprites:
I also manually edited the “arms up” pose for these sprites. Because of the layer ordering, by default the head and hair pieces are layered above the body and arms, which can appear strange with some combinations. For these premade characters, I edited the arms of that specific pose to appear above the head on the front and side views.thanks!
These small edits are examples of the complications mentioned above in the first section of this document. These premade characters can work as examples for when you come across situations where you might need to edit your own characters