You are correct. SEGA of America is located in the same building and suite number as Atlus USA. You can see that here: http://www.sega.com/corporate
And here is the Contact page for Atlus USA, showing the same address: http://atlus.com/contact/ (This has always been their address in recent years, so that would mean SoA moved into it, unless Atlus USA also operates as them)
There is also another SoA on the SEGA corporate page, which is probably now the main building for the SEGA company and brand in America.
The address also appears on the back cover of Dengeki Bunko (image here: http://puu.sh/kVQHB/a843e7001c.png), with SEGA of America as the company title, so it seems the companies act as one another depending on what game is being distributed.
I'm guessing that the John we saw is John from Atlus USA acting as PR for SoA.