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Image rotation is more fine-grained. The free transform rotation is just buggy.

Photoshop will save layers to TIFFs. I think it's a proprietary data block--other images may only see the composite image, so if you edit it in another program and save it you'll probably lose the layers. For more complex PS documents I'll still use PSD.

I've never been able to do anything useful with SAI. I never redraw stuff from scratch; I do all fixing with clone and patch tool...