To me, dumping files all over the drives is messy, sloppy, and bad practice. Always has been and always will be. Someone just wants to copy MS stupidity into linux.
I think some features from the FHS predate Windows and even Microsoft. Having every file belonging to an application in the same place is insecure and makes it more difficult to support things like multiple users or one user with multiple PCs, especially if some of them are thin clients.
In my case every one of my vdr boxes are dedicated single-user htpcs. For me, having all of vdrs files in one location makes backups very easy to create & restore. Additionally, navigating to whatever file I need is simple -- no hunting or trying to remember what is where. My only big wish as far as setup goes is vdr getting real & solid server/client support, and the good news there is that unless things have changed, it's actually on Klaus's TODO list. But anyways, thanks to ONEDIR and LCLBLD, I can completely ignore FHS with no hassle at all.