Pretty sure it [main board serial header] was built for hackers since the USB port provided a way to send commands for debugging.
It could have been a legacy of development where all the pieces of a USB interface, software and specialized parts for the final product, were not initially available and the serial port was easier and faster to build and use for development work. From what I see, somewhat cumbersome high capacity equipment is used as USB hosts, from the purpose of that standard, for disk drives and the like, which also makes radio connection to Neato's usb not so easy, if they needed that. Initially the USB section just got added onto an existing board design left to be refined in later revisions, which finally happened. They might have had some test equipment left over as well, which later got revised to USB. A sort of leap frog pattern of changes, add something first, then later drop something. Maybe it is to run both things for a while until the new stuff is checked out more, like new accounting systems run in parallel with old, before committing to the advance.