Well, the UNS put up automated defenses, which may be slowing down the "everyone." However, Petey thought it was important to keep everyone from being killed in the fighting, but people were being killed already by the automated defenses, so it's already too late to completely prevent that. Anyway, presumably there is a big rush to stop the killing and Petey is in a big hurry to shred the planet and yes, everyone is probably trying to get through the defenses as quickly as possible.
Yeah it doesn't make much sense that there isn't more of a sense of urgency, but that's nothing new.
Meanwhile Captain Landon is AWOL, but doesn't seem to be in any trouble. Bala-Amin seems to either not know or not care that the UNS research ship that had scientists aboard who seemed to be reporting to her has been stolen, even though she seemed to think that the research they had been doing was extremely important.
I'm not sure why they wouldn't just terraport Cindercone wherever they want the tree to go. The only problem would be if Cindercone couldn't terraport close to the destination. Maybe they've been completely surrounded by hostile TADs. Using it as a cage would still require a receiving terraport cage at the destination which would limit where you could send the tree.
However meta-logic probably trumps any in-story logic, so I agree that they probably will use Cindercone as a terraport cage. (HT just revealed that Cindercone is a terraport cage so it will be used as one and it's not as if in-story logic matters much.) If they actually are going to use Cindercone as a terraport cage, they probably are terraporting the tree into the can of sky, which is the only place a receiving cage would be located, AFAIK. Presumably, they would use the one Sorlie was investigating. The Esspies will probably be moving into the can of sky.
I have no idea why someone didn't think of the Esspies moving into the can of sky at the very beginning of the arc, though. Murtaugh's contract with the Esspies was stupid (in several ways). If the balloons wanted the scientists to be able to study the ball of PTU strands, then the balloons should have been the ones to offer the Esspies something in return for permission. But of course, that's just in-story logic.
About the only reason I can think of for using the "world movers" as terraport cages, rather than terraporting the loaded world movers would be if the DMEs couldn't sense the terraport cages, but could sense the terraports that didn't use cages. I hope that's explained sometime.
If they are going to use terraport cages, I would think that something more like Kevyn's beach head cage design would have been better than big spheres. The idea would be that you would just throw gravel into one cage and have it fall out of the other. The cages would be moved around to wherever they were needed.