From the data you gathered, I would tend to say that encoded / in an URI are meant to be seen as / again at the application or CGI level.
That’s to say, that if you’re using Apache with mod_rewrite for instance, it will not match pattern expecting slashes against URI with encoded slashes in it.
However, once the appropriate module/cgi/... is called to handle the request, it’s up to it to do the decoding and, for instance, retrieve a parameter including slashes as the first component of the URI.
If your application is then using this data to retrieve a file (whose filename contains a slash), that’s probably a bad thing.
To sum up, I find it perfectly normal to see a difference of behaviour in / or %2F as their interpretation will be done at different levels.