Simulink allows you to manually set block sizes and wire routes; however, Embed sets block sizes and draws wires automatically.
When you translate an MDL model into an Embed diagram, Embed positions blocks at the same coordinates that they occupied in the original Simulink model. Simulink blocks can be rotated both horizontally and vertically. Embed allows horizontal flipping only.
In Embed, you can move blocks around to make the wiring path more legible. You can also add wirePositioner blocks and, if required, flip blocks horizontally, to improve the legibility of a diagram.