I was wondering if this is a similar issue as raised in this thread.
I went back and updated the script in the thread to include an alpha padding feature.
The issue came up for me when importing, not exporting, so I have not tested eishiya’s suggestion. It wasn’t clear from the above whether export sprite sheet features resolved this. I think it’d would be nice if the user had some discretion regardless of the stage in the workflow: import, editing, export.