Following on from this question....
We know that to add a new template into DNN, we simply export the Portal Template, then edit it accordingly.

My question is, how would you restrict these templates to only exist for specific portals? So Portal A has templates C,D & E. I have done the obvious of creating a Templates directory underneath the portal directory, and copied in the appropriate template file, but DNN is not picking this up. I have also noticed that if I navigate to this new directory using the file manager, the directory does not exist?

Am I on the right path, but potentially have the wrong permissions?

Thanks for that confirmation Vladan. After posting my message, I decided to check the source code, and modify it slightly to include reading in the templates at the portal level.

FYI: /admin/tabs/managetabs.asc.vb
arrHostFiles = Directory.GetFiles(HostMapPath & "Templates\", "*.page.template")

I added
arrPortalFiles = Directory.GetFiles(PortalSettings.HomeDirectoryMapPath & "Templates\", "*.page.template")