I read the online manual and could not find anything about being able to set the subwoofer phase, is this an available feature for those with passive subs?

If you have a passive sub and a crossover/amplifier without a phase control, your only option is to reverse the polarity of the sub by reversing the speaker leads. I have passive subs and have never run into a situation where this was not flexible enough to get flat bass response.

So basically your saying it does not have this option?

It's not that I worry about getting flat bass response, it's that I want the sub to be in phase with the rest of the speakers. Do you think that with this pre/pro, 180 degrees is enough control to fine tune the sub to be in phase with other speakers?

Having continuous control over the phase of a subwoofer is highly overrated in my view since you can only correct for one (or a few) points in the room. Ideally, you want to use a spectrum analyzer like TrueRTA and a calibrated microphone to achieve the flattest response - and this is not necssairly with the subwoofers "in phase" with the mains. You can achieve "in phase" by using a simple 1 1/2 volt battery connected to the speaker but this is not necessairly going to achieve the best response in-room.

I have never found that control finer than + - 180 degrees to work any better toward the flattest response using an RTA than with continuous control over phase - and my subwoofer system is "rather substantial and complex"

Most active subs actually only have 0/180 deg phase switches anyway.

But I do prefer subs that have a variable phase control. Sure, you only get the phase correct at one point in the room, but that's right where I'm sitting.