Question when downloading new models

[Your Computer]

Hmm well if that was the case then I don't think the normal Amnesia files would load properly...

But anyhow, custom_stories is listed in the resources.cfg by default, so it's not really a problem either way.

It's not listed there by default. You probably had it there for so long that you forgot you added it in. Normal Amnesia files wouldn't load if their folders weren't listed in resources.cfg. Since they are it is not an issue.