crApple does it, but at least you can drag and drop any file/folder anywhere you have write access.
I'm not sure if Timeshift has the ability to do individual files/directories. Never needed it for that. Whenever I roll back, it's cause I did something stupid, or an update didn't play nice and I need to wait for people smarter than me to fix the problem
TM has a feature that lets you time scroll in a 3D like layer of the folder where you invoked it.
You can restore a missing/deleted file/folder or restore it anywhere you want.