[Milhouse]

Checking in fixup.dat, I find the script is planning to rename the Defendor files with prefix alright... BUT it's using VIDEO_TS as the Movie-Name element.

Yes, VIDEO_TS isn't supported - I'll need to add support to mklocal.py, but it's unlikely to be added soon.

Best approach (as I see it now) is to remove the Movies_VTS folder from the Library, correct the naming and location anomalies, and then "Scan for new content".

I'm pretty sure you can eliminate the VIDEO_TS folder entirely so that all files are in the "Defendor (2009)" folder. This would resolve the issue with mklocal.py. You'll need to remove, clean and rescrape your VIDEO_TS movies. Try one and see how it goes before doing the rest.

In the context of a VTS rip, does it make sense to name the artwork as if there were a single video file (ie: with Movie-Name-prefix) ?

I think it's personal preference, but it does at least identify the artwork unambiguously which is a plus, and it's why it's my preferred naming convention.

In your opinion, are there other practices I should adopt for keeping the artwork under control

Nah not really. I just try to avoid remote artwork as much as possible so I run mklocal.py on a regular basis to ensure that any remote artwork (I use Artwork Downloader after scraping new movies to find logos and clearart for older movies) is converted to local artwork.