Here’s the best thing to do. Whenever the woofers are going to be playing the exact same frequency response, measure them as one driver (woofer). So measure the frequency response of both woofers playing together and their impedance. Just make sure they’re wired how you’re going to wire them at the end (aka series or parallel). Then measure your Tweeter response. Finally measure them all eyes together to find your z offset. So in Xsim you’ll actually only have one woofer and one tweeter that you’re messing with. Once you do this, I think all your issues will go away.
For anyone that’s reading this, that might not know. When taking a measurement like this, just keep your mic at Tweeter level when you take your frequency response.