I have used fuse-overlayfs in the past for my lan party setup to have multi-user installs of games that insist on writing to their own installation directory. One big trouble I ran into was performance. For this reason I have eventually replaced it with AUFS.

This was ~7 years ago though, I have been using AUFS ever since and did not test the in-kernel overlayfs yet. The big complicating factor was that I ran everything off nfsroot and did the fuse-overlayfs mount on the client machine side, so every file lookup sent two file lookups to the server. Two games that were horribly slow due to this were Warhammer 40k: Dawn of War (+expansions) and Crashday. Both of them have a directory with thousands of files and open them with case-sensitivity mismatches. The regular load time of the games was in the area of seconds whereas the fuse-overlayfs solution took minutes to load the games.