Sorry for the delay. You're right, there was an issue with texture packing being skipped. This is fixed in 3.2.00. We hope to do a release in a few days. Until then you can use an older version of Spine, eg:
/Applications/Spine/Spine.app/Contents/MacOS/Spine -u 3.0.00 -i /Input/Folder -o /Output/FilenameWithoutExtension -p /PathTo/SettingsFile.json
I'm not sure when the problem with CLI texture packing was introduced. You could also try 2.1.27. Note when running 2.x.xx after running 3.x.xx, there will be an error the first time v2 runs. Just run it again and it'll be fine. This is an unfortunate problem with v2 that is remedied in v3+.
