I would recommend following Matt Hamsmith's solution. If it's an issue to implement, then why not create an extension method that implements this in the background on the AppSettings class?
Something like:
public static string GetValue(this NameValueCollection settings, string key)
{
}
Inside the method you search through the DictionaryInfoConfigSection using Linq and return the value with the matching key. You'll need to update the config file though, to something along these lines:
<appSettings>
<DirectoryMappings>
<DirectoryMap key="MyBaseDir" value="C:\MyBase" />
<DirectoryMap key="Dir1" value="[MyBaseDir]\Dir1"/>
<DirectoryMap key="Dir2" value="[MyBaseDir]\Dir2"/>
</DirectoryMappings>
</appSettings>