True, Autopilots and advnced autolanding systems ARE FAR MORE ACCURATE[/i] than people. (Well, not the Soyouz ones....)
IMTU only final docking is manual. Most other activities, including slipway entry, are automated.
And a few reasons why it is that way IMTU:
1) Confidence (above)
2) beacse that way there is a human committing the ship to station regs by manually docking
3) since you're already in the slipway, you ca't do THAT much damage
4) it "proves" you've a competent ship-driver aboard.
5) it gives practice for those situations where you HAVE to do it manually
Now, many hgh ports IMTU also have a dummy dock, usually automated with a 0.1G drive for course correction... specifically for pacticing manual docking and approach. Often not in orbit around the mainworld, but a satelite thereof.
As for visual recognition, the OTU hasn't specified, aand semi-canon sources (MTSSOM, MTJ) indicate that the cameleon hull is the norm, not the exception. I don't recall any running light requirments being mentioned.
More important are the things which require vastly more precision than skill. Like docking bays, and airlocks.
IMTU, these have a consistant markingn pattern light-wise. Docking bays use quad fresnels (one each side) to tell you visually) how you're doing on bay entry, and lightstrips around the door. Red, Green, Blue, Amber... L, R, D, U respectively, from the standpoint of the bay door. All blue means down is straigth in, all amber means striaght in is up the ship's gravity plane.
As for "Flying by Autopilot", the 3I either does a lot of it, or the skill for pilot is actually "Autopilot Programming".
MTU is designed to accomodate the former,