That’s an interesting question. Having good file naming is the solution to a lot of issues, and it’s The Gospel that directory structure matters too. Who are you to question The Gospel? 
I’m curious too.
The Movie and Series (TV) scanners definitely look at the directories. For TV there’s definitely an assumption that it’s Series/Season.
With “perfect” file names, I’m not sure if the directory structure matters as much. So I agree - that’s an interesting question.
There’s comments in the .py like this:
# Not a perfect standalone match, so get information from directories. (e.g. "Lost/Season 1/s0101.mkv")
So it’s clear that directories can help matching if file naming isn’t adequate.
There’s a big update to the Movie scanner in the current PMS beta, and I have no idea how it behaves.
For the “old” scanners, you can see the Python code. I’m not sure where this gets put on different platforms, but on FreeBSD it’s something like:
.../Plex Media Server/Resources/Plug-ins-fede5bdc7/Scanners.bundle/Contents/Resources
I haven’t looked at or thought about it enough to say that it DOES or DOESN’T have other pros/cons.
For movies, the Plex documentation encourages directories, especially IF you are using any of the additional features - especially local media assets or extras.
I fear that your question is going to be drowned out by “matching P90X is weird” answers.
P90X and Jillian Michaels are probably the “best case” for workout videos because they have been added to some of the databases. For others I thought this was a good discussion. It doesn’t address your scanner/directory question, but it shows some of what other people have done for workout videos and has some good links.
