I'm reminded to the Genesis Device from Star Trek: The Wrath of Khan and Star Trek: The Search for Spock. Flash-terraforming in science fiction is notorious for how often it will break appart and just end as a work of hubris.
In part because of the simple reflection from real life that some things need to take a certain amount of time and that while times can be shortened with trickery or improved technique, it can only be done so a degree, but eventualy if pushed too far it will just produce something inferior to what is created "properly" with time and care.
Plus more common knowledge in modern day about just how complex and fragile an eco-system like Earth's is, reflecting into how Sci-fi writers treat the act and longterm requirements for terraforming a planet to the point where it can sustain itself.
In addition to that, how many of these Omegas are actualy "smart" in the scientific sense of knowing about the requirements of creating a habitable world. What is required as basis, what problems do certain pre-existing environments create, what is required for longterm sustainability of the eco-sphere, how long do the chemical reactions and organic growths need to progress until the necessary atmosphere is created, etc.
None of them strike me as Mark Wattneys and judging by his reaction experts like Doctor Nemesis were not involved in planning the whole thing either. Instead it seems the Omegas were just flexing their muscles and eyeballing the whole thing based on instinct and rough knowledge.
So terraforming Mars in an hour just based on a general idea of how it could be done and taking time skippers at every opportunity might have just produced an impressive looking big building but standing on a weak foundation, with missing cables and pipework and eventualy the number of necessary repairs and improvements might pile up to the point where it would be better to let it crumble and start again properly.
In europe there are a lot of stories about shoddily rushed housing after WWII which barely lasted 20 years at times, while even many damaged "cheap" pre-war buildings were still sturdy enough after repairs to last into modern days (albeit not as comfortable as dedicated newer ones).