Thank you for reporting a bug to Unity.
After reviewing the behavior, we've confirmed it aligns with the current design and intended use of the feature. We understand this may differ from your expectations or workflow.
You can refer to our documentation on Sprite Atlas Inspector window reference: "Disable this property if you pack Canvas UI elements, to avoid UI elements rotating."
(see https://docs.unity3d.com/6000.3/Documentation/Manual/sprite/atlas/sprite-atlas-reference.html)
We will close this case as 'As Designed'. If you have feedback on how the feature could better meet your needs, please let us know - we value your input and consider it in future improvements.