Updates docs to use getter methods.

Continuing from #1892
I think it would be helpful to explain why here in a few words since so many people do this.  I assume you mean something like this is not recommended

```
var myRegion = app.r1;
```

For instance...

> Regions are also attached directly to the Application instance, but this is not the recommended usage, because it increases the chances of naming collisions and, in the future, regions will be stored in a container object.