Hey mate, glad you're getting use out of the tool and appreciate the comment. I'd love to see what you've cooked up using it.
Regarding your point about the animations - yes it's likely your root motion is causing the animation rig to shift in world space. In order to capture the frames I'm actually manually stepping the animation and capturing the render result really fast (you can sometimes see it pop up when rendering). I'd recommend avoiding root motion entirely because the camera itself won't track the object, leading to potential challenges when trying to fit all of your frames within the render space.
You can probably tell by the UI but this is built in Godot itself. I'm a big fan of the engine and seeing a plugin to automatically load the outputs of FlatPixel into it would be great :)
Your feature requests are very helpful! Especially the point about arbitrary turntable mode settings - I had been struggling to find a way to set that up that was intuitive. Maybe just an integer slider with the "number of angles" would be enough...