When mysql chroot and web server chroot are different, we can still connect to mysql in our web app using 127.0.0.1, i.e. via tcp/ip. But localhost/socket will not work, since the two chroots are different.

If mysql chroot is under web server chroot, We can then use localhost/socket to connect to mysql from within webserver chroot in our web app.

Performance wise, socket is better than tcp/ip due to the overhead of tcp/ip.