That's weird my save data and custom content folders are all located in the same folder which is "C:\Users\"myname"\AppData\Local\VotV". It has always been this way as well at least as long as i have played the game which is about a year. I think you can set your own custom content file path in-game in the settings.
Viewing post in Voices of the Void 0.8.2 Bug Reports
I'm glad that it works for you, but that's not the point of a bug report.
The default settings, aka blank asset path, leads to the game creating and searching for a false Appdata path.
Meaning there is some bug or discrepancy in how the game gets Appdata while accessing custom content, vs how the game gets Appdata while accessing save data etc.