So this is what I encountered:
I found that when running Dimensional Eclipse, and have the new collision code and/or merged index buffer enabled, it seems pretty much any mission that has the Tethys/Narayana as well as loading it in the Tech room just causes it to lock up when it starts to load it. Funny part is the old, unoptimized Tethys works perfectly fine.
Secondly, when I enabled the merged index buffer code, I get this:

Fancy new cloaks they got there. So, just to make sure the collision actually worked, I ran into the invisible buddy Hurricane.

Great success! I'm in intense pain. But...am I the only person who has all the ships go invisible?
But even with both of those features off, I got around a 12 FPS boost in the more intense missions of Dimensional Ecplise (22 - > 33 FPS on Nexus Station).