But can this lossless rotation process account for padding not being in the usual place (lower right corner presumably)?

I'm not sure if this is how JPEG implements it, but in H.264, you just have metadata which specifies a crop (since H.264 also encodes in blocks). From some quick Googling, it seems like JPEG also has EXIF data for cropping, so if that's the mechanism that's used to crop off the bottom and right portions today, there's no reason it couldn't also be used to crop off the top and left portions when losslessly rotating an image's blocks.