Been doing a little power supply research for an SLI project too. I've found the 12v rails are completely separate on these dual rail power supplies. There seems to be some slight variations though.
Antec says their 12v1 powers the CPU and motherboard components - like a Vcard's power though the AGP socket. In this case, 12V1 would be powering your CPU and would also be the only source for your SLI'd Vcards (as you describe there are no additional plugs with these.) In this case, your concern seems well founded.
Enermax says 12v1 is dedicated to the CPU alone. That leaves 12v2 for motherboard components (like a Vcard's power though the AGP socket) and drives, peripherals and everything else. In this case, your concern seems still well founded.
Also, you noticed the numbers don’t add up too well. I added up the advertised ANTEC numbers from those charts. Antec’s 18 amp/12v rails and the XXamp/5v, etal. I got 780 watts available watts from a 550 watt PS. So I asked. They went on and on about this and that. Did I just not get it, or was there just nothing to get? (. . . probably a bit of both). One thing for sure though. The dual 12v rails are isolated. One rail doesn’t share excess capacity with the other. It seemed to me, that even with the biggest dogs, I would be buying a shared 20 amp, 12v rail'd PS for my Vcards. That’s not enough for me.
I decided to forgo the dual rail PSs and go with a strong 12v single rail (Still shopping). I decided the best bet was to get something that can keep the well filled, then just let everybody stick in a straw and take what they need. That way, I don’t have to worry about anyone coming up a bit thirsty.