Nothing wrong with that other file - it is caused by something 'strange' which has been around for a long time.
Some files DO have their own sub directory in whatever Mods folder active - but, it simply wont replace the original default(s) intended and append its data & values to it. Thus, why we get doubled items.
In these cases, the "only" way to actually get ONE file as the correct set detected (while the other is discarded) is to use it from the *Data* folder straight into the root and ignoring the supplemental other folders.
Mind you, there are some files which MUST (or should) be used from their provided folders for them to work as they should. A few of these being; HeightMaps, Invasions & Scenarios, etc.
There might some other cases... but, i haven't tested them all yet. I guess it is a matter of trial&error unless SD coders can provide this entire info -- exactly -- to any of us.
(PS; Shouldn't this thread be transfered into the Modding section, moderators?)