3. Impulse. Sins is Linux compatible. Impulse isn't. You aren't going to bother with making Impulse Linux-compatible. That means that the people wth Linux will have to get their patches and micro-expansions some other way. Like through piracy. Dumb move.
For one thing, I don't see Linux as being offictially supported - a quick glance at the system requirements, and I don't see Linux listed anywhere. I would say that the compatibility is more accidental and not something that should be counted on in the future.
In addition, Impulse is Stardock, and Sins is mostly Ironclad. Sure, they worked together, but ultimately they are still two different companies and not obligated to support the same platforms.
. . . and finally, if they were to port to another platform, it would make a lot more sense to port to a console or to the Mac. Sorry, but Linux's market share is pretty abysmal, especially when it comes to games.
And I would be willing to bet that every game, no matter how "modding friendly" it is, has some sort of hardcodes or limits to how much stuff you can add in. They probably all have a point at which the game can't take anymore, and it just crashes. Some games just allow more to be added than others.
It's mostly a matter of complexity and performance. The more generic something is made, the more "layers" it needs, adding some complexity to the game and decreasing performance because of the increased overhead needed to keep track of all of that stuff.
What 4X doesn't have a ship builder?
The big ones made by the big companies - pretty much every Civilization game. I liked the ship builder in GalCiv 2, but I'm under the impression that a game with a ship builder is the exception, not the rule.
In any case, it's ultimately up the the developers where to spend their time. Please keep in mind we are talking about small development teams with limited resources.