An excellent point. (I use bellows and a wide variety of adapters on my Canon bodies and have seen this too.) The chipped adapter (usually for 1.4x or 2x teleconverters) is necessary to retain auto-focus.
The other scenario and a big one to watch out for is that if you use an "auto" adapter and a manual lens, the camera will (almost always?) lock up when you actually take the pictures. In some cases the picture will be recorded and you have to cycle power to get control back (e.g., film-bodies, Rebels, 60D). In other cases, the picture will not be recorded and you still have to cycle power (e.g., 5D3).
The auto adapter (auto-focus control and/or aperture control) is often associated with teleconverters (or tele-extenders) or extension tubes. The issue is that the tube tells the camera, "what's attached to you is auto". But then the lens breaks that contract. Often, you can "modify" the flanges on the adapter with a dremmel tool to convert the adapter into a manual focus, but electronically controlled aperture. (I've done this, and you have to be REALLY careful (and accurate) with modification.)
I don't think I've ever been able to get an AF lens and 3rd party adapter to provide focus confirmation (but I haven't really tried that hard to get that). Also, I've not had any problems (ever) with pure manual adapters, which includes various mount adapters (like the M42-EF) or reversing adapters (for macro).