Just a suggestion, but perhaps you could add a "realistic" and lore friendly terraforming option in the settings that you can enable to make specific types of teraforming impossible and others unable to be done unless you build terraforming buildings related to them.
For instance, if there was a world with the hot or cold modifier you would not be able to remove the condition by terraforming the planet unless you had stellar reflectors in orbit, and if the reflectors where removed the condition would return in short order as the surface would again be unprotected. Or if you wanted to make a world have a mild climate you would have to construct an atmospheric processor first, and likewise the atmosphere must be constantly processed to keep the mild conditions in effect. (maybe have it so the maintenance cost is drastically lowered if you have access to domain tech, to allow players to terraform worlds into low hazard conditions without nullifying the benefits by the massive 50k maintance costs, or perhaps have it so that the terraforming buildings have lowered maintainance costs as time goes on because the planets conditions become easier to modify as they settle down)
Also make it so that you cannot change a planets type by terraforming but still allow better conditions for farming/organics/volatiles via the terraforming option, like you just terraformed the planet into the same type normally. Perhaps make it require the use of an Eisen division because you need to engineer new strains of flora, fauna, and microbes to take hold on the planet and you would need labs to create such things, unlike the reflectors and processor however, once the new strains are developed you can shut the lab down as any new developments can be handled by local lower tech labs (ie. space termites get in the space corn, colonists develop space raid, this does not need an Eisen division)
Like I said this should be an option, not what the mod should be, this just feels more in line with the lore as taking a jungle planet and suddenly turning it into a water world or vise versa in a couple years just feels so wrong to me. This feels better as your not preforming centuries of work in a couple years, your just taking existing conditions and using the degraded but still advanced tech of the sector to improve upon them, not playing god by throwing comets into water and creating continents. (you can explain why it only takes a year or two to improve the farming/organics/volatiles condition by saying that the only areas effected are those within direct use of the colony, the world will be taken over by the new strains from the Eisen division in time but that is decades away.)
Or you can do what I do and just refuse to change planet types and require the specific industries before I allow terraforming to occur, then keep them around after it is done. That is easier to do and requires no programming lol.
I will admit however that it does make exploration much more necessary and keeps good planets rare, it just makes it so that your good planets can be made better and the edge is taken off the bad ones.