Flat harness is a completely new model that references your cabling.
You have control over what you want to "fan out", you do not have to do this for all cables and wires.
There is an automatic option that tries to fan out in all directions based from your starting point. But you can also select a point where you want to fan to. Then you can select a new start and end point to fan in this direction. In the end you have only those cables in your flat harness, that you need and you can automatically attach the connectors you want to see.
If you want to have multiple separate flat harnesses (for being less confusing), you can simply create multiple flat harness models.
Talking about at least 2-3 common locations: In some harnesses with multiple common locations there may be closed loops. This is always a situation, where the user has to take control and solve those loops. Harness MFG allows you to open the loops where you want them opened, in order to be able to create a flat representation.