Chainfires update notes for 2.64 and beyond... (I'm installing 2.66)
A major change in setup is that the ZIP installer will try to detect 6.0 firmwares that can be rooted without doing a systemless install. In other words, a root that modifies only /system, but not the boot image. If this is possible, the installer will install into /system (unless you override via "echo SYSTEMLESS=true>>/data/.supersu").
This may catch (a) firmwares that allow sepolicy reloading from /data but have a locked bootloader and (b) custom firmwares setup to handle this. Regarding the latter, while it is not as clean as systemless, those running custom firmwares are more likely to want to modify /system anyway, it is less likely to mess with updates to those firmwares, and it prevents the necessity of reflashing the ZIP after each kernel switch. Of course, the kernel's SELinux policies must support this! See this thread for details for devs.