Had a friend that due to an accident had a left 1.5 cm shorter, he was telling me that he was setting the saddle height as if he had both legs equal then lower the saddle 7 to 10 mm to compensate the shorter one. The next thing was that at the beginning he said he had a lot of pain obviosly but he sucked up until the pain was gone forever.

Another friend had a similar problem, when he seats his hip rotates, 5 mm shorter right away. He sets the saddle considering the shorter leg. so if you look at him from one side he is ok, from the other side he look kinda too low in the saddle. He live with that.