I think you are neglecting the fact that it is possible that some clans are NOT centered around banditry and robbery. Some clans WANT to be identified because they want to be seen as helpful to the civilian population. Take the free medics for example. I'm sure that some free medics would testify that by them having the XML and "uniform" it has actually saved their lives.
Along with the whole "Its better to run as a civilian group than an identified clan" it is true to a certain extent. But you must also consider that this is the truth in real life. History has show that when a "group" of people are hidden in plain sight, in this case the civilian population, they have an advantage that a clan would not have. But I don't think this mean's that they have an unfair advantage. The clan is able to organize much better, they usually are better armed(not always the case), have more numbers, much better communication, they are more resilient in firefights. Think of the Viet Cong in the Vietnam War or the Taliban in Afghanistan.