The catch can won't work anymore with the same vacuum hose routing as N/A. Since your boost is pre-throttle body. If it were a TRD S/C it would.
Your best bet is to have both valve covers route into the can then have a vent to atmosphere filter on it.
Such as this.
Hmmmmm
I don't understand why wouldn't it. There's still vacuum when the throttle is closed, which should help extract the oil vapor. Also, the problem with having the breather on the passenger side hooked up to the catch can is that that breather does not have a PCV valve, so boost will leak into it. Unless I put a check valve there, or like you said let it vent to the atmosphere.
My catch can has two inlet ports, I can use it for both heads. But I'm questioning the wisdom of it.
How did you fit that fitting on to the passenger side vent?
Edit: What I'm going to do is remove the check valve and see if I start collecting oil again in my catch can. If I do, then I know the chech valve was too restrictive. If still not collecting oil, then I'll hook up the other passenger side breather to the catch can and put the check valve back on.