There are plenty of cases where you can't just change the file layout. And the GPU filesystem is being implemented by someone else, so the choice is: migrate your data to another filesystem OR fix the data-in-files layout, even though the files may come from completely different source than your application, the layout may be a standard or other applications may depend on it, or you can't easily change it for another reason.
If you can get the data into the GPU-native filesystem, you can change the data layout at least as easily. The point is there is some sort of data ingestion pipeline involved.
I think the main benefit here is not having to do memory copies through the CPU, which frees up memory bandwidth for other things.