Well it sounds like the files you are getting are a little layer happy.
A maybe overtly simplistic explanantion on my part. There are others who have written about this way, way better than me.
Architectural drawings tend to be used as the base for different disciplines. So the different layers are created so that when an MEP or PE or civil uses our drawings as a base, they can screen the colors of the x-ref by layer.
Plus we tend to use our plans for reflected ceiling plans (rcp) and sometimes as the roof plan. So we have the different layers we can turn on or off depending on the type of drawings we are using. Either that or everything is a separate file and x-reffed together and then somebody will wonder why we are file happy. So walls are a certain layer but if you are doing an RCP, you have to be able to turn off or freeze the doors and windows and then fill in the gaps with a header. Same with the roofs, you don't need to see a lot of the stuff below, so you freeze them. It's also why sometimes, people do draw roof plans on their own file. But we have many different types of sheets we need to generate, so the diferent layers help us control what is displayed. Some firms use their own layer standards, some have whoever draws it standards, some have no standards, some don't know what standards are, some use the AIA layer standards, some the national CAD standards and some use a combination.
Decent companies will have a standard that is available for everyone on the team, including consultants to use as a guide and understand where everyone is coming from. Ours was based on sitting down with our regular structural, civil, MEPS over a few days to hash things out. basically a standard based on consensus. It seems to work and everyone is happy to date. And since it was done this way, if their caddies complain, we never have to say a thing. They jump down their throats themselves.
Maybe when Revit does become the industry 900lb gorrilla, we may have this worked out. Then we get to create a new bunch of monkeys.