Note that AUFS has been succeeded by overlayfs which, unlike the various earlier union fs attempts, has actually been merged into the kernel. I'm not sure where it stands with regard to flaws
It's pretty flawed - for example, if you open a file read-only, open it again read-write and the write to it, any read from the first file descriptor won't show the writes. The corner cases don't bite people under most circumstances, but when they do they're awful.
That sounds like a fairly normal structured file/multiprocess workload, not much of a corner case there :(
its still pretty raw. check out cve-2015-8660, which basically let unprivileged users bypass normal file permissions without even trying. it's fixed in mainline now, but still hasn't hit a lot of distros.