Aside from how the gameplay of it would absolutely suck.
This is very subjective. Many would disagree.
But I never said you need to buy and deliver everything yourself. I just said that having a specilized colony ship is far superior in both gameplay AND realism.
Because now you have a slow target you have to protect. Because now you cannot colonize as fast or as easily (colony ships and colonists need time to prepare). Because it neatly explains why the colony is even possible and where the people come from.
This is very subjective. Many would disagree? I mean, we can throw that right back at you. But really, it is an objective truth that it bring no new gameplay. If you ever brought a freighter with you you've experience everything having a new "colony ship" would entail. As for realism, the problem is not establishment, its growth. People could establish small colony with flipping sailboat here on earth. Now they are doing it with enough supply to rebuild a capital hyper advanced spaceship AND a huge amount of heavy machinery
What do you need to make a colony? Well, people. Check. Supplies for those people to use to build things. Check. Thats all colonies really need. The fact that they also need heavy machinery IS the acknowledgement that they might need something on a scale larger than what ships need.
Depends on where you colonize. Just dropping people and some supplies on a planet does not make a good colony. As colonization efforts go, it is a terrible, terrible start, even on a mild terran planet.
Thaago already said it, but maybe you glanced over it without reading. We. do. not. know. whats. in. the. supply. Its not "magic" its abstraction. Just maintaining a car here on earth require hundreds of different pieces, fluid and whatever. It would be absurdly stupid to have us deal with all the possible thing a space-faring civilization thousand of years in the future would need to maintain their nano-fabricated incomprehensible ships. In fact it would be objectively stupid unless you wanted to make a totally different game. So we get supply and heavy machinery and you put in it whatever you need to maintain your suspension of disbelief.
If you can survive in space you can survive on the ground. Supplies encompass everything that keeps combat ships operational and repaired, from food to air resupply to filters to machinery to...
The requirements are totally different for starters. And you are protected in the ship, while you have no shelter on the ground. Building shelter/habitation for 1000 people is not fast or simple. Which is why I said PREFABS are necessary.
Also, supplies for running a ship are not the same kind of supplies you need for a colony. Or does you standard stock of supplies include farming tools, seeds, animals and such?
A colony ships solves ALL logistical and logical issues, since it's basically a town that lands and deploys - it takes care of all the immediate issues and serves as a center of early colony operations.
Spaceship building is right now quite harder than shelter building. Might change in the future, but we got no reason to suppose one or the other. Our standard supply definitely contain food and heavy tool are sufficient to strip an entire research station. On top of that it is established lore that tool are fabricated as needed(see fighter ship too). As for seed and animal , well farming is an industry you do not start with so it is also established lore that your initial supply are not sufficient for farming.
These spaceships run on miracle flux that ignores conservation of energy/momentum, they can teleport through space, they have energy shields, they can enter phase space, adjust the flow of time itself: the tech level here is far, FAR above where you need to be concerned about building air scrubbers. Hell, supplies could just be a combination of common base atoms + power packs for replicators for all we know, the tech is certainly advanced enough for it.
Space magic never is and never will be a good answer. It's a cheap way out for the laziest of the lazies. Magitech is no different than saying "Because God willed it".
Space-magic is the answer given in every single work of fiction that include tech level beyond what we can reasonably imagine in a very near future. Its the only possible answer anyway. Coherence/consistency and the general respect of currently known physics rule is the only thing that slightly differentiate hard from soft Science fiction. But all use space-magic with different amount of style. There's a lot of literature on the subject, but for entry level you probably can't go wrong with
https://tvtropes.org/pmwiki/pmwiki.php/Main/MohsScaleOfScienceFictionHardnessIf you feel like colonies are too cheap: fine, increase the price. Require the user purchase a once off Atlas for... crashing... reasons. But what you call 'profoundly stupid' is just a failure of your imagination.
Or perhaps the failure is yours?
No u? Seriously what is that answer. Thaago original post was already a perfect rebuttal of your comment about it, I merely reused what he said in the hope that you would actually read these word. Any call to "realism" is either a misnamed consistency problem of the lore or a lack of imagination. I think our post demonstrate beyond reasonable doubt that we do not have consistency problem with the current implementation of colony start(balance is another thing). I will leave the required conclusion to your own imagination.