Ok I got it working. There's one texture that's still unaligned but I'm sure that's an images issue.
The problem is that I'm packing multiple texture sets (head, outfit, etc) and was pointing to the images folder instead of images/outfit, etc folder.
Solution that worked:
(for command line noobs)
In Windows Powershell navigate to C:\Program Files\Spine. If navigating down to program files from the C drive, cd "Program Files" avoids spacebar errors. Using Spine or Spine.com didn't work, needed to use ./Spine.com to run spine commands
./Spine.com -i <texture1 path to the directory the pack.json file is in(ex: localPath/images/outfit)> -j <project directory> -o <output path> -n <output file name> -p < texture1 pack.json file path>
./Spine.com -i <texture2 path to the directory the pack.json file is in(ex: localPath/images/outfit)> -j <project directory> -o <output path> -n <output file name> -p < texture2 pack.json file path>
...etc
My use case is that I'm actually creating 4 outfits from 2 textures input into a single material to save time & space, and using only 1 atlas file to store the multiple texture atlases. So I need to align the 2 outfits plus texture masks and atlas switching doesn't fit my use case.