As far as camera Auto modes (including A,S and P) are completely useless if they don't detect the strobes, I never use them with this strobe setup.
A, S, modes do not ever take the fact that a flash is connected in to consideration. Even when you are using a genuine canon speedlight or the built-in flash. Try it. Set the camera to A, S, and see what exposure the camera chooses. Now attach a flash (or raise the built-in flash) and see what exposure the camera chooses. The camera will choose the same aperature and shutterspeed in both cases. (so long as shutter speed is below flash sync speed)
This is actually very usefull. The camera will choose the shutterspeed or aperature that will expose for ambiant light (the background) properly (underwater you usually dial in a stop or two negative exposure compensation so the water is nice and blue). The flash then fills in the forground.
I'm not sure if my camera (a Canon, but not a 5-D) will trigger the pre-flash in manual mode (what for?

) even when converter is powered.
Yes, Manual mode on the camera has nothing to do with the flash. In all exposrue modes the flash works identically. TTL works exactly the same in manual mode as it does in A or T.
What for, you manually set aperature and shutter speed. The camera will then adjust flash to properly expose the forground.