Hopefully you'll get ears on in the form of REW measurements soon to see what's really going on.
A few other general thoughts...
You need to differentiate specs/ground plane measurements from those of your own in-room response target, accounting for the sub's acoustic roll-off and the gain resulting from corner placement. The SVS in one configuation may be flat to subsonic territory in a ground plane measurement, but put it in a corner and it will have a dramatically rising response as frequencies decrease, which will require attenuation/eq to bring back into line. If it were me, I would choose the configuration of the SVS that yielded the best compromise between extension and flat in-room response *without requiring additional eq*. Armed with REW, that won't be guesswork, and it will help you choose the appropriate config for your particular room, whatever it ends up being.
There isn't really any musical content at 12hz. There is music content where your sub and mains cross, so getting that area correct is somewhat more consequential to your ear's enjoyment than a few hz of extension on the low end. Using REW you'll be able to dial in the sub-to-mains crossover far better than by ear, getting you closer to optimum level matching, crossover frequency, and phase adjustment.
*target response curve...you had asked previously if flat response is what to aim for. I think it is, at least for system calibration purposes (optimizing speakers/sub response in situ) and for the sake of accuracy. Once the subs are properly integrated with the mains, *then* global eq can be added for preference. Global eq won't scramble your REW efforts with the sub-to-mains crossover, but merely goosing the sub level independantly of the mains will.
In room measurements are typically a real mess, fair warning.
Are you using the antinode thingie? It seems a bit limited if it's only used on the sub, and could add latency due to the ad/da conversion. The Arcam has no bass management facilities at all, does it?