Just to confirm I'm not crazy:
http://prntscr.com/9dc51p
Everything was started simultaneously and chosen to ensure the starting timers would be the same if there were no bonus. The patent labs are next to laboratories, the upgrade labs are next to toolshops, and the offworld is next to warehouses. The hacker array is not next to offices, but a different test next to offices didn't give a bonus either.
http://prntscr.com/9dc74v
Another screenshot just to confirm the timers are running at the same speed, and they are. I also tested placing advanced buildings next to the wrong module types and didn't find any speed bonuses for any combination.