Yeah, the save directory is the same for both running the jar and running the exe. I personally do use the exe because I usually play on my laptop and it doesn't like running the jar in fullscreen properly, but even when I used the jar .toa-data was there. Directories starting with . are often hidden, but for whatever reason this folder in particular never has been on my Windows systems.
If you do end up running the exe as I do, you can just drop .jar files from new updates in there and it runs without having to update any of the other files.