I ran the jdupes duplicate file finder in my PhotoTranscoder directory.
Some files were duplicated hundreds of times, more than tripling the size of the directory.
I used jdupes -L -R PhotoTranscoder/ to convert the duplicates into hard links, and recovered the extra space. (I’ll delete the folder if this breaks anything.)
I tested by browsing with a few Plex clients. Everything seems to work. Of course, many new duplicates were created. 
My guess is that the PhotoTranscoder Cache filenames may be overly unique. I wonder if it’s generating filenames from File+Dimensions+Client+User, and I wonder if it should only be using File+Dimensions. (Or maybe they’re random!)
Is there any possibility it’s something like that, @drzoidberg33?
If that’s the case, it might also be a major speedup!