Pretty much have everything nailed down with regards the MK 7 with regards option and settings, basically most things, but there is one aspect not quite grasped and what information have read has been fragmented and so still not clear, just when think understood, it seems contradicted.
And not having the R yet means cannot 'tweak' and try for myself, but do not want that process to be a long one, and would rather take the definitive advice and optimise exhaust flaps quite quickly.
But where to start? Settings for when in comfort and normal and just running around town, does the shift of the DSG to S open the flaps then, and you go to 'Race' or do you have to select 'Race' to get to that engine profile?
Also the sound aktuator? Think it now is adjustable? So how does that fit in with the optimising of the flaps to get that sound we all like to here.
So what seeking is
!. Some general advice on how the flaps operate and to what purpose?
2. What settings there is to make in menu to achieve what end?
3. How the moving of the DSG to S and D affects flaps
4. How moving the car to manual (paddles) affects flaps.
Sure this would be useful information to have in one place for others moving models to an R
A while ago I asked on here whether we should have a section for R specific info, but there wasn't much appetite for it.

Anyway, here's my 2ps worth.
If you are in Race mode then the gearbox is automatically in S, and all other settings are in Sport. For the other modes - Eco, Comfort (if DCC) Normal - the gearbox is in D and the other settings as per the mode, however, if you stay in the mode but just snick the gearstick to S, it will open all four flaps giving you the full real exhaust sound. In Individual mode you can customise everything to your preferred setting with a choice of Eco, Normal of Sport for each item.
The soundaktor volume is adjustable in Individual Mode only. It is the option called Interior Engine Sound and you can choose, Eco (lowest), Normal (mid volume) or Sport (loudest), In the preset Driver profiles the soundaktor is set as according to the mode and cannot be changed, but Individual mode allows you to have the soundaktor volume as you wish at one of 3 settings in combination with the other settings. So for instance, if you want all four flaps open and full exhaust, but don't want the full blown fake noise of the soundaktor, you can set Drive to Sport which puts gearbox into S (all four flaps open), then set Interior Engine Sound to Eco, which is the lowest and least obtrusive volume.
In answer to your specific questions:
1. When the gearbox is in S then all four flaps are open. When the gearbox is in D, only the inner two flaps are effective, and you will see evidence of this in the build up of carbon on the inner flaps, more so than the outer flaps.
2. My answer to this differs slightly to iandjm's answer. Two of the driver profiles do affect the flaps, by means of putting the gearbox into S. Race profile sets everything to S, including the gearbox, therefore all four flaps are open in Race mode. Similarly, in Individual mode, setting the gearbox (Drive) to Sport its the gearbox into S and opens all four flaps.
However, it should be noted that if the car is in Race Mode or in Individual mode (with Drive set to Sport which is the gearbox in S), after the ignition has been turned off, when it is turned on again, even though the driver profile remains active, the gearbox defaults back to D, so just 2 flaps, and to put the gearbox back into S (4 flaps) you need to either nudge the gearstick down into to S or reselect the mode again via the driver profiles - by cycling to the desired profile - Race or Individual.
3. Moving DSG to S and D. As iandjm says. S opens all four flaps and idles higher revs and Stop/Start is deactivated. Gearbox in D opens only the inner 2 flaps, idles at lower revs, and Stop/Start is active by default.
4. Reiterate what ianjm says - if in D auto and move to manual via paddles or via stick (moving stick to left) the 2 inner flaps operate only. If gearbox is in S auto and you shift into manual (paddles or stick) then all four flaps open.
If gearbox is in D, the very simplest way to open all four flaps at any point is to simply nudge the stick down into S.
There is a VCDS mod that will open all four flaps permanently and this has been well documented on the VWROC forum. A search brings up numerous threads on the subject. You can also unplug the exhaust valves which will also result in all 4 flaps being open all the time.
Sorry to link to another forum, but this thread may be of interest to you.
http://www.vwroc.com/forums/topic/12970-exhaust-in-four-pipe-mode/