Yup, embedded... but, read on --
Spore-Ships! Reverting the effect of that particular ship would probably simply be a matter of TotA module "creation".
As for DA stuff, i have actually expanded the Terraforming branch for X-Worlds(05-F) to include new concepts which would require a fourth level (or more, btw) of enhancements to surface tiles. This, in fact, is not far out from the Genesis device mentioned since it does boost the actual default values.
And yet again this is another Hard-Coded feature that i wouldn't be able to alter without patching the exe for myself. Although, once the new version is out... i fully expect players to witness the potential and even, try convincing SD_devs to implement the extra tiles.
(PS; this
system is thoroughly explained in another thread "About Custom Planets" further down in the forums here)
Now, the actual magic of transforming a PQ0 to colonizable variations could simply involve providing the regular "InhabitableByAll" tag an extra slot where a toggle could mean improvable by such a device. A sort of indirect Sixth Extreme!

But that would defeat (or greatly lower its intended impact) the whole concept or purpose of Extremes, don't you think?
We DO have development perspectives with any of these, once the Colonizing branches allow for true control over these surfaces.
If there is one priority area where planetary assets could be recoded with new features, it is the PQ1 rogues (wasted, but tricky)... anyhow that's only me, thinking & wishing aloud.
Don't forget overall Planet Quality potential is also a tech driven quest and those advantages must be earned, when a powerful Genesis device could certainly tilt this fragile balance into unpredictable results; namely, i could well predict any huge maps being flooded by AI controlled super-genesis ships to take over anything & everything in the galaxy.
What about Saturn? Gaz Giant, isn't it? Right now, nobody can colonize it. And yet, how many small Moons around it could?
Expand your mind on this - A planet with Satellites would become a Star system on its own... and this, without ever using a Genesis one-time fits all solution.
Strategy of expansion, i'd say. Rather than being spoon fed PQ0 (no longer nil, btw) surfaces with new tiles.
Gimme a way to boost my Homeworld from PQ18 to PQ33 (!only 15 more tiles - 5 Y_O_R schemas each!), instead!