I can confirm, that any mix of Bellerophon hull(secondary) and pylons will result in ship nacelle lopsidedness.
I've also noticed that most of the Bellerophon tends to vanish or turn extremely primitive at full zoom out.
As for the windows... Actually, from what I can tell, the issue with the windows selection is that they seemingly do not apply to ship parts not from the same 'batch' as the last dropdown box:
intrepid, cochrane, discovery VERSUS bellerophon - the last dropdown choice lets it's group have the proper windows while the other group defer to option 1.
But that's just a minor issue compared to what I've noticed the past few days...
A major graphics change as to the on-ship rendering of windows has been made on Tribble, when I don't know.
This change allows the windows and escape pods to change color based on abilities. For example, they now blacken entirely when using Mask Energy Signature.
HOWEVER, this change has also resulted in ALL SHIP WINDOWS to pixellate and vanish entirely over model distance, instead of only becoming slightly blurred due to distance. No amount of settings tweaking has resolved this.