The non-dockable megaships, of which there are a lot, don't have owners. They come under the temporary responsibility of the controlling faction of the system they enter, but are not technically owned by them.
This is almost certainly the way the Zende megaships work. They want to be able to stop any random faction in Zende taking them over and hitching a ride into Synuefe, which I imagine would definitely cause some issues. No reason to create a way for megaships to be tied to factions that hold other assets, when they can just hook it up to the same mechanism as those non-dockables where they fall under the controller's jurisdiction. We'll know for certain come Phase 3, anyway, as the status panel will show what asset of Zende they're defending.
Was Segnen's security/economy also reset?
Yes, which is why I'd expect a similar effect in Zende for all other factions. Otherwise, the security reset was entirely (besides ZP) localised on the CG system - the place in danger of Lockdown.
Why would they do that? This CG doesn't need to pass anyway - if it fails, Segnen can blame Zende for mismanagement of the system and claim that it would be better if they were in charge, then start the war that way. Sure, there then wouldn't be a Guardian Tech Broker at the outpost ... but that's not essential, and they've quite happily left stations with poor services after partly-complete CGs before.
Conversely, if they actually wanted it to pass, no chance of alternatives ... they could have set the tier 1 level much lower in the first place.
All true, but that doesn't mean Frontier see it the same way. That sort of adaptation was largely what I was hoping to see, but it sounds like they had nothing prepared.
Setting low tiers is a common tactic to ensure that CGs pass, but they appear to have forgotten to account for the fact that this isn't a normal CG, or they've VASTLY overestimated the number of people who would be interested in this. Maybe Tier 1 is low, relative to other trade CGs, but when your main method of gathering cargo is relogging in a SRV...yeah. Last I checked, still on one pixel of progress, and most people seem to be leaving after 20-30 tons.
Probably doesn't help that this wasn't explicitly advertised as a CG until after the megaship ferry had left, either.