The answer to your question regarding whether the Arc AT is "sewn through" rather than baffled might be found in the following excerpt from the FAQ at Nunatak's site:
"Baffle spacing, which is the horizontal distance between the individual down filled chambers, is standard 5" on all bags including the Arc Line. Baffle height, on the other hand, determines the vertical size, or thickness of the insulation and is also known as loft. This measurement can vary from bag to bag."
Note that the above discussion of baffling, both height and spacing, is described as the standard on "all bags including the Arc Line" — which would seem to pretty clearly include the Arc AT.
Frankly, given the prices and construction time for their quilts, the possibility that Nunatak makes any quilts as a "sewn-through" rather than baffled never entered my mind. It would certainly be well to verify that fact, if there is any question, at the time an order is placed.
As for your other question about whether a custom order to Nunatak for an overfill of down will actually increase the loft or just stuff more down into the same baffled area, I can say based on my experience in ordering a custom Arc Alpinist from Tom that an overfill of down is (or at least can be) accompanied by an increase in baffle height that allows additional loft.
Back when I ordered an Arc Alpinist several years ago, the standard baffle height for the non-customized Arc Alpinist was 2 1/2 inches. I requested a two ounce overfill with the order, and Tom informed me the baffle height would be increased to 3" to allow for extra loft from the overfill.
I also requested two other modifications for my quilt, one of which was loft-related.
First, I had the quilt made with a differential cut for the liner and shell to help eliminate loss of loft that might occur by the liner pressing against the shell.
Second, I had the length of the quilt fitted in between the standard regular and long lengths since my height fell right at the break point for the standard sizes.
Best to keep trying to contact Tom to obtain authoritative answers, though. From my experience, I found him to be very patient, helpful, and knowledgeable. He provided great advice on considerations that I never considered, as well as giving answers to all of my questions.
While my quilt was being built, Tom even provided me an excellent Arc Alpinist demo to use on a trip I had planned for some time. Design & workmanship for the demo was great, and likewise the custom quilt that I later received.
Hope the above info helps a bit.
JRS