Hi,
First of all, I believe BNC connection is a better link than AES/EBU, which the real reason is for VERY LOOONG cable drive, but in short distance, offers no meaningful advantage, in fact, could be disadvantage, because the signal level from AES/EBU is huge (8Vrms), and that has repercussions in generating more ripples and more jitters, ceteris paribus, plus the fact that XLR connector itself are not true 110-ohm impedance.
I read the manual of the World Clock module, and if what RME stated is accurate, it should offer a significant clock improvement. I would think since with your RME investment, and the sophistication of the RME system, my suggestion is to stick with the RME.
In general, the PCI bus offers far better interface accuracy and option, but with a high complexity for both the design side and customer side (opening up PC, can't use with laptop, etc). I don't think you should give up the RME and start all over with the new USB module given the same cost. The World Clock module is plug-and-play and has no impact with your other settings.