If you are only ever running one ASP.NET application on a website this is not an issue. However, if you are running a site which may have an application at the root and other separate applications running in sub or virtual directories, then Settings inheritance could be a problem.
You can read more about how config files get inherited on msdn but here's a tip for stopping settings in the root app from getting inherited. The <location> tag is the only tag I've come across which has the inheritInChildApplications attribute. So to target the main <system.web> just wrap it in the location tag as seen below.
<location path="."...