Azalrion basically it adds realism in my opinion, it also adds variety, if I could I would also add artefacts but I'm not sure how I would go about that as nothing like that seems to be built into the game whatsoever. That might make the game more alive and exciting. If I can make it an option then that would be great and I will so it keeps the original bits and pieces and adds a new feature that is optional.
We always need to keep in mind, how to represent the realism in the game too. It's not as simple as simply settling on the first idea that pops into your mind, or copying it from another game or a string of games, because it might not work very well in this game. For all we know, metallurgy, sociology, and other research disciplines already contribute to the tech required to build more efficient stuff on planets. The increase of productivity might be because people found new ways to deal with the environment and make it workable.
If this is true, then the argument becomes not one of realism, but which brand of it you want, culminating in whether you want options to research each and every single planetary type, or to group them together into one research item, or spread them out among several evenly. For my position, I would take the latter. This isn't SoaSE, or SotS, the number of planets in your domain run into the hundreds, it's simply not possible, or a highly repetitious task that the computer or the game design as a whole should have taken it for you.
You do realise I was referring to humans/Earth, us. We've can't even colonize the bloody moon yet let alone reach and colonize another planet. Considering it does say at the beginning of every game that your civilisation has reached space flight. Only just reached space flight so...Now you could take that to mean we can send a rocket into space or a satellite or you could take it to mean we can send out a ship that can fly through space at will and sustain its crew for somewhat long periods of time. Even then that's I would say simpler then COLONIZING a planet that could fry you, poison you, or freeze you to death. As you would then need powerful technologies to fight back the heat or the cold (far more extreme systems then what we have for places like the north pole or at volcanoes). And the poison could be dealt with maybe but then building on it that's another question entirely.
The main reason we can't exactly reach the moon is because of the incredibly high costs of shooting things into escape velocity. The price more or less being down to several thousand dollars for every kilogram you get into orbit, and this isn't calculating the costs required to push it even faster beyond orbit. This is compounded by us not having any real reason why we should go to the moon in the first place. If we were, as a collective species try to colonize the moon, I don't think there'd be much holding us back in terms of construction. It's basically building air tight structures which we already do on earth like antarctic and underwater habitats. The main difference would be that on a body where the atmosphere in near absence, there'd be little to no maintenance that you'd see on underwater or in the antarctic regions.
All it'd really be is to construct starship like structures that don't leave the planet you're sitting on, and the civilizations in SR already seem to be able to do that almost without much trouble at all. It does seem to be quite consistent with what's already in the game.
As for planets where it's freezing or filled with magma, I think most starships are already equipped to deal with these things, they seem to travel close to the sun without much trouble after all, and I can't say it'd be unreasonable that the people who go on to distant planets to make lives for themselves expect it to be easy. The modification and streamlining of the human body ought to be quite common in those circumstances.
In any case, it's quite rare that an entire planet be covered in magma, but even if it is (possibly because it's too close to the star), SR civilizations do seem to be able to build things that handle that quite well. Even if a sizeable chunk of the planet is molten and shifting magma, I think SR does a good job of depicting limited building space for this.
Above all though, I think you're missing one vital part of the puzzle, that being that the colony ship also functions as the main city. Like a dome city I believe, it's equipped with everything required to build more cities as well as the facilities required to expand.
As for your realism argument, I think it ultimately comes down to how the game abstracts reality. There are several ways to do it, lore wise, mechanics, or even graphically implied. Personally I think the limited number of build slots fit this quite well. I think most people underestimate just how big a planet can be, it's astronomically low that there'd be not enough space on the surface to build anything at all, and the SR populations on these planets are hardly the jammed packed situation we have on earth. All but the largest planets have populations matching the US without research into sociology. One might even hazard a guess, that sociology IS the research done to make planets more habitable, but unlike what you're proposing, all of the research is rolled into one to save time and space.