The change is intentional. But, when upgrading a profile without the change, the profile-specific files should be copied (leaving behind the original copies) to the "Default" folder. Not sure why they weren't in your case.
If starting with a fresh profile, all the profile-specific files and folders should be in the "Default" folder without any extra copies in the parent root folder.
You can rename your "Opera Next" folders while Opera is closed and start and close Opera Beta to see how things should be now. Then, you can move those new Opera Next folders out of the way, put your old ones back and fix things if you want. But, you can't switch back to the old folder layout.
Just note that there's a bug where the splash screen might show every time Opera starts unless you put a blank file named "Preferences" in the root of the "Opera Next" folder. There's some splash screen code that still looks for it there in that old spot.