Nah, can't be anything like that.
You're right, it can't. Arduino hasn't cornered the market on PCBs with off-grid headers, as evidenced by this very product. Any assclown with a PCB design tool can do it. It's just the poor saps using veroboard who are screwed. Hanlon's Razor applies here -- never attribute to malice that which can be adequately explained by stupidity.
As for the end connectors, that's a total cockup. They should have at least made some of them coplanar so you can make expansion boards that need more than one set of pins. Maybe one to each side and then three on the end. But I still wouldn't buy one, this chip is just too pretty to live.