Is there a way of avoiding "LoadFromContext was detected" errors

Question

I have my catalog pointing to a sub directory of the app domain's base. But I get an exception "LoadFromContext was detected" explaining this is a bad thing to do. It says it is better to load from the base directory. But mixing my extender parts with the rest of the app's files will make managing them vary difficult. 

Is there a way around this? I tried using 

AppDomain.CurrentDomain.AppendPrivatePath("Providers")

But this get a compiler warning telling it's obsolete and that I should be using 

AppDomainSetup.PrivateBinPath

But this only works on creating a new domain.

Is there a configuration setting where I can supply the sub folder?