Well over a year later, the answer appears to be Yes, they will work.
After some friends did some measurements, some personal research, including a look at my own B7 A4, I decided to take the plunge and get a set of S4 RECARO seats. Worst case, I would have a nice upgrade for my 06 A4, putting more "sport" into it's sport package ;) .
I know the S6 seats will work just fine in our cars, however I have never been a fan of the look of them, as they reminded me of "vader" seats from the E36 BMW M3, or "cone heads" as I personally call them. Personal preference, but I have always liked the square shoulders of the B6 / B7 RECARO seats.
As far as the seat hardware is concerned, They bolt straight in without modifications to the rail at all. Outside of that, the remaining work all depends on what generation seat you get.
In my case, the RECARO seats came out of a 2005 S4, a car that did not have a factory occupant sensor installed, so as opposed to buying one on ECS or the dealer, I simply removed the perfectly good one from my factory seat. The transfer is relatively simple as explained on
this link . The Process is quite similar, however you will need to retain your seat belt buckle from the A6, as well as your factory wire loom protection as it is quite handy and saves you from some taping work. The connector types are also different, yet the actual pins inside the connector are exactly the same size as ours. Simply use a pin tool to pop the wires loose from the S4 connector, and pop them into your saved, or new C6 floor connector.
Only issue I am having now is related to the airbag having 2 wires on the B6, versus 3 wires in my 2010. With this, the airbag light is on sadly, but I hope to work to resolve this while keeping the Airbag functional in the event it is actually needed.
So far just the passenger seat is installed, however, Heat, power, occupancy sensing (dash light included) are all working as they did with my stock seats. Looking forward to installing the driver side, and finally have adjustable thigh supports in my A6, as well as proper bolsters. Personally I love the new contrast, and intend to keep my tan door cards and light wood, while I change out the seats and a few other interior bits to black. It's not as if the C6 is totally lacking of black in their tan interiors from the factory anyway ;)

RECARO Seat with my occupancy sensor bladder installed, as well as the sensor control module for the sensor and seat belt monitor.

The bladder itself.
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