Good question, something I hadn't thought about for mine yet either to be honest. I don't see why it would cause any issues for one of them to be vented to atmosphere but who knows.
Being you said you don't have a good path to the hot pipe, which way do you have the manifold? I've seen some who have flipped the manifold so that the gates face downwards as opposed to up, not sure if it would help or hinder your fitment issues but it could be a potential option if you wanted to be able to run them both to the hot pipe. I'm also sure you've thought of this but just in case you hadn't.