I pulled up TX pin of CP2101 to it's internal 3.3V regulator and connected to 328p's RX through a diode. USB 5V is also connected to 328p through a Shottky diode. So the CP2101 is not powered through the arduino board.
I used unregulated 5V supply (which is more like 15V) to power the arduino board to use it's diode, fuse, and internal regulator.
1. It should be fine if you disable 3478A extensions (OX0 command). Most* GPIB lines are not actively pulled high in atmega. I assume 2 scenarios:
1) external USB controller is used, then atmega board does nothing.
2) hp3478ext can be used as a controller for other devices connected to HP3478A externally.
Although, in both cases GPIB signals should stay within allowed atmega pin voltage.
* I should check the code, and tell you how it works exactly. May be I haven't put enough thought in it...
2. If it's a buzzer, it doesn't require PWM. Initially I used piezo speaker (which requires a driver to sound properly). When I switched to the buzzer, I left pwm so the buzzer doesn't sound loud. I can add eerpom config to it so you can tweak it.
UPDATE:
IEEE 488 specifies maximum signal level as 5.25V. This should be fine for AVR.
All GPIB signal lines in hp3478ext are driven in open collector way. There's no strong pull up.
DAV and SRQ lines are weakly pulled up. Current hp3478ext firmware pulls DIO low when inactive. I'm going to remove this behaviour, because it would conflict with an external GPIB controller.