Don't get me wrong - I think this is fantastic, really, and I can't wait to see it all.
However I think that having 2 bays is more unworkable than 1. There's the size issue, of course, but also with your pass-through, the level above opens with a circular railing balcony overlooking the bay. I think if there were 2 bays, what you would see would be a half-circle, as the other half would overlook the other bay.
As I said I think the only realistic solution to this is to move engineering and the intermix chamber further back. Although we have Mr Probert's drawing, and Shane Johnson's deck plans, I think that what we see on-screen has to be the guide. There is no on-screen evidence that main engineering is at the extreme forward of the secondary hull, or that the chamber is mounted between the torpedo tubes, or that the chamber connects to the impulse crystal (or even if it is a crystal) and much logical evidence to suggest that none of these things are true. The existence of the corridor leading out of engineering would indicate that it must be located further back to allow for its passage.
It would be interesting to hear Mr Probert's thoughts on this...