That is the way it has been for a while now even with Splat.
They made the Per Project option the default. I don't think there is a way to shut it off.
It was probably because every one wanted the per project as default because the old global audio folder was a bad idea and made it hard to back up songs. There used to be a lot of threads from people who had a huge mess and had lost track of their audio files.
I used to have to manually make a project folder before saving a song. Now it's done for me so I certainly like the feature the way it works. Saves time.
Example you open a midi file and then SAVE AS to a Normal ( CWP ) file it will create a folder and put the CWP and an audio folder in there. Done. Ready to work on.