DEVINSHERIDAN Thank you for showing us the video! I was able to reproduce the issue in Spine 4.1. After checking the changelog, we found that the fix added in Spine 4.3.00-beta prevents the position from changing due to generate.
Generate and other actions that remove any deform keep the mesh's scale.
https://esotericsoftware.com/spine-changelog#v4-3-00-beta
Unfortunately, in Spine 4.1, it seems there is no workaround for the issue where the position changes when using Generate, other than changing the image size itself and avoiding the use of scaling.