In UE 5.4, I tested the Property Matrix and confirmed that LocalTransform and CustomPivotPoint can be edited. You need use “Details” tab instead of the property tab.
If you have a large number of Sprites that need modification, my AssetProcessor plugin might also solve this issue. It’s a versatile bulk-editing tool for asset UProperties, including those only modifiable via C++. I’ve verified it can batch-edit Sprite LocalTransform and CustomPivotPoint properties. Below are the YouTube video link and FAB link—hope this helps! 
