Looks like the setup would sync the external PSU with the MP's PSU although it could be a mess to route the cables. Unless you have plans to use your external PSU to power two GTX 690's, what I don't understand is why didn't you choose the booster X5 like most others did? It is more compact and can be easily installed in the second ODD bay, and has a built-in molex plug to sync with the main PSU.
I had initially considered this internal PSU, but having read dozens of threads on getting the GTX 690/Titan to work on their Mac Pro's, more users just seemed to advocate the use of an external PSU, especially a high-quality one. One of the most important considerations was that I couldn't come up with a decent solution to run the power cord from the Booster X5 (i.e. from the optical bay) out of the MacPro4,1 enclosure. Lastly, the GTX 690 being a 300W card, I thought would have the option to power an additional GTX 690 in the future if I decided to scale into another one (although please correct me if I'm wrong here that 660W is enough to power two GTX 690s).
Have you used the Booster X5 successfully with any cards?