This really doesn't have anything to do with nanomachines...SPINE isn't based off of nanomachines. It's basically a data transfer system. If the nanomachines comment was directed at the SPINE comment anyway.
Using SPINE a neko can pilot/operate a starship in real-time during combat. Accessing all of its sensors, weapons, and flying it. Even if the neko were only just piloting it's still vast amounts of information from a large number of sensors being feed simultaneously into it's brain, arguably more than a single (static) personality would contain. These sensors report the condition of the ship, engines, engine temp (as it affects propulsion anyway), shields, spatial position, orientation, speed, incoming enemy fire, outgoing fire, all friendly ships, armor, fighter-craft, shuttle-craft, etc., all of that that belongs to the enemy, open communications (closed too if the pilot is also the comms officer), and any other things that might be relavent, all at the same time. Further this information is updated real-time so that effective ship operation can continue, further it even /returns/ information on how the ship should maneuver, fire, etc. (list appropriate commands to the ship here). Sure some of these roles can be performed by additional crew members, but the amount of information transfer is immense.
When you look at a static file, even a file such as a personality, you have to realize that it pales in comparison when compared to all of this. The file might be twenty to thirty times larger than a single second of combat data but when you consider that that single second of combat data is constantly updated, faster than light travels perhaps, then you grasp just how fast these blazing data transfers really are. Taking a full 20 minutes, the same time as a backup/restore, would be completely illogical.
Consider that ST tech is older than SPINE, and must work on all species. If ST tech was as fast or faster than SPINE then it would probably be used as a transfer medium for the information instead of SLICS then it's successor the SPINE system. After all, if it ain't broke why fix it?
edit: anyway, that's the reasoning and logic behind it. I digress, I don't care either way since I don't play right now. I enjoyed making the original article though, it was very fun. Hopefully you guys find it useful.