Is ScaleData by layer?

[leetde]

Hello, I have a question about the tutorial in https://satijalab.org/seurat/articles/seurat5_integration. The tutorial advises splitting the object by Method first, then performing NormalizeData, FindVariableFeatures, ScaleData, and RunPCA.

Are the ScaleData and RunPCA functions performed on each layer separately, or are they performed on the combined/joined layers?

Similarly regarding the last section of the tutorial on SCTransform, is this performed on each layer separately if the object is still split by Method, or is the function performed to the combined/joined layers?

Thank you