With recent kernels you can combine overlayfs and btrfs. btrfs subvols/snapshosts have their own costs, they can get slow once you accumulate thousands of them

With recent kernels you can combine overlayfs and btrfs. btrfs subvols/snapshosts have their own costs, they can get slow once you accumulate thousands of them (it's fine if you just use a few at a time). But you can create a single btrfs subvolume, store your overlays in there and then delete the subvolume when you're done.