Because "just scale it up" is not a valid solution for everything.
You don't see 3km long mega-freighters on the sea, do you?
Because sea freighters aren't supplying the demand of a group of 10s of billions of people (size 9-10 colonies)? They are supplying cities and maybe countries, which would be like a size 6-8 colony. If there was a need for bigger freighters, they would build them. There is also a lot less room in the ocean than in space, so there are additional downsides to size/lack of maneuverability of large vehicles.
There are tens of thousand of freighters out there. A single freighter sure as hell cannot supply a country, so your own argument falls flat.
The simple answer is that bigger is not always better and that there is no need for a single super-mega-freighter to supply a city/country, when you can have dozens or hunderds do it more economically. Simply put, there is no need for such impossibly huge ships - neither in our world nor in SS. And large things have downsides both in space and in ocean.
You really wouldn't want civilians to have ships that are TOO big anyway, given that you can turn any single one of them into a continent cracker.
But your second argument (it's ok for lore and gameplay to not match) cuts to the point. If Alex thinks that player facing large scale trade is not good gameplay, then he has every right to not include it in his game, regardless of any argument about whether or not it makes sense with the lore (i.e. realism arguments). If we can agree that it's ok for lore and gameplay to not match, then there is no point in arguing about this any further.
Another silly argument.
Any single discussion can be ended with "well, if dev wants X then there's no point in discussing further."
People here are discussing what THEY think is good gameplay.