Final ISO when using Flash

This is right as far as I know. On the D700 with an SB600 attached, it would behave the same. You can set your ISO manually, the number you set will become the base from which Ato ISO then rises to the max you set in the menu (assuming it hasn't changed with the D600)

If you want more ambient and less flash, push the base ISO up to whatever you can bear, at the same time you can dial down the flash, both on the body and on the flash (not sure about the sb400)

Without knowing your settings, I'm assuming the flash fired at full power because it could. Just dialling down the flash will raise the ISO automatically, and include more ambient, if that's what you want. It wil also make a darker image, on the whole, which might be more realistic. Experiment using a bounce card, if you can tape one to your SB. They can work well by sending a little light straight forward and bouncing the rest. If you're trying to shoot a person in front of you in a room, using ttl-bl and centre metering, this can produce nice results. So long as ttl doesn't make them blink..

Getting a nice result is almost as easy, and more repeatable and understandable, by using manual flash. It's easy to control and you won't get blinkers - I'm going way off topic. And ttl is great, I use it all the time, I'm just saying  if you want predictable results, go manual everything. Only give the machine control over things it can do the way you want them doing.

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