[XLA] Make ShapeUtil::PermuteDimensions() properly permute layouts.

Although there was no API comment explaining what PermuteDimensions()
intended to do with layouts, the intent seems to be that if the input
shape has a layout, then

  TransposeIsBitcast(input_shape, PermuteDimensions(input_shape, perm),
                     InversePermutation(perm))

is true.

This was not previously correct.  (I can't really say what the old
behavior was, although maybe there's some clever interpretation of what
it used to do.)

PiperOrigin-RevId: 203290794