Wow man, I feel so damn stupid for not noticing the "fast" checkbox XD, I guess it doesn't optimize space so well but that's not a problem right now.
Yes the game is pixel art and it has a lot of raster animation. We mix raster and skeletal a lot and we use spine for positioning stuff. It allows a lot of cool tricks (that only devs notice, and only some of them XD).
With the "Fast" option selected the texture packer is much much faster, glad to see the suggestion of the progress bar 😃.
Thanks a lot Pharan!