I can certainly understand that as a building novice, one feels totally insecure. Some people just have consistent luck (lots of relatives and friends in the trade, inherited land, simple and level ground, standard taste, low demands, etc.) and some are building in Munich and really have to buy everything and already pay 400,000 bucks just for the land and are satisfied with only a 40,000€ garage.
With a land price of 250,000, I would also assume that craftsmen are no longer being thrown at you; those times are long gone even in the East. At least in the areas that are booming, and Berlin definitely counts as one of them. As far as I could see from the invoices, we had the cheapest craftsman at 35€/h and the most expensive at 79 and some change. Craftsmen are scarce and they know it too.
I would definitely rely on the judgment of the local pros, but with healthy caution. I actually find your approach quite smart. In the end, hopefully, the worst case will not happen, but it also certainly won’t happen that suddenly everything becomes cheaper or even just as expensive as calculated. If your general contractor has been building houses for 20 years and hasn’t coincidentally not built any for 5 years, then he will surely have an overview, just like the architect, etc. Nevertheless, I would probably take the warnings here seriously... people probably don’t write that because they find it funny and have nothing else to do, but because they might have already fallen into the cost trap themselves and want to warn others. We ourselves didn’t build new because it would have simply been too expensive and we wouldn’t have been happy with the location of the targeted property in the end (too far out). But even the initially targeted costs from the prefab house builders for a rather small and simple bungalow were so high that it would have simply become too expensive. Especially with all the things that weren’t even on the table at that time. That would have been way too hot for me too. Nothing could have gone wrong with us, otherwise, we wouldn’t have been able to pay for it anymore. So we just didn’t do it and then bought a simple existing property and renovated it ourselves. But we were insanely lucky to get something relatively cheap and there were no incidents – which brings us back to the topic of luck^^. I know in Berlin, it’s actually almost hopeless and I can probably save myself the following: But if new construction is too risky, unpredictable, or expensive for you, then see if you can and want to make compromises. Maybe an existing property, or "just" a condominium or whatever. Before you can’t sleep at night anymore, that is sometimes the better decision.