Hi, Generally, Macbooks are already isolated as most of the laptops. Because of electrical laws, you don't have any current way between the primary (AC line) and the secondary (DC line to the laptop) of your computer. However, if you prefer to use a opto-isolated communication, I saw USB isolating devices from OLIMEX, I guess other manufacturers sell this king of devices too. Apple II is an old kind of device, it probably works with 5V so using the level shifter is important.
The libftdi library only provide access to low-level functions of the FTDI chips (it is the free equivalent to libftd2xx). The devices enumeration as /dev/ttyUSBx is handled by the kernel modules to emulate standard UART over USB. That's the reason why you were able to program the Papilio even before installing the library. For your enumeration problem, I can only guess that updating your kernel allowed newer drivers to enumerate the FTDI as two UART. Have a nice day.