Arduino controlling high voltage DC source, Opto-Isolator

Disclaimer: This is in response to the posted circuit, not an answer to the question of control with a PWM. I just didn't have room in the comment.

Any special reason you need the optoisolator? As your circuit currently appears, I don't think that your D5 connection to pin 5 of your optoisolator phototransistor will supply the kind of current you want. In addition, synchronization between the two PWMs will likely cause you pain (What if the D5 PWM is always off when the D3 PWM is on and vice versa? No sound! You need to average your signal, and feed it into a buffer. You'll also likely want some hefty capacitance on your V+ line to the micro and buffer so that your supply voltage stays smooth.. However, the connection to ground and the connection to D5 totally eliminate the purpose of the optoisolator, which is to allow the speaker circuit to be at a different voltage than the input. This might be useful if you had the speaker at a remote location from the Arduino, and want to run a low-current differential signal on a twisted pair out to the speaker, which would be powered from a different power supply. As is, you might as well just connect pin 6 to D3, and just use the transistor, completely ignoring the "Opto" part of the circuit.

See the output circuit for the AVR335 appnote linked in my other answer for a circuit which effectively drives a speaker with a PWM. The filters smooth the output signal to something better approximating the input (With a rolling average), so that you get a smooth wave rather than a rough digital square wave. You can remove the unary gain amplifier, that's just to remove any feedback from the microphone (Which you don't have).

You really want some filtering and amplification on the output -It'll sound absolutely terrible if you don't. You know how those talking greeting cards sound? They have filtered outputs. Your speaker will sound worse than that if you just connect it to the PWM. I was previously assuming that you were using the phototransistor to isolate your output and transfer it to an amplifier/filter circuit running on a different power supply, but a straight connection is going to sound really bad.

Your two configurations are equivalent in output drive, although obviously the output logic is inverted between them.

The decision therefore comes down to which polarity is more fail-safe and idle current issues. Config 1 fails to high and takes active current to be low, with config 2 the opposite. Use whatever works best for your system.

One reason people knee-jerk to config 1 is that a switch between a line and ground with a pullup is more common. It is often convenient to be able to ground one side of the switch. Far more things come with built-in pullup resistors, as apposed to built-in pulldown resistors. If this signal were going into a microcontroller, for example, then R1 could be internal to the micro and you'd use config 1. In that case logic polarity doesn't matter since micros can generally deal with low or high equivalently.