If the scripts are actually stored "in" the construct and simply executed in the local client, then as far as we are concerned I don't think we should really care. So long as anybody with rights to the construct can access and execute the scripts.
To answer your bullet points, because some of things you're listing aren't applicable in Dual Universe. This will be compiled from the information we know about from the AMA responses as well as various interviews and other responses here on the forums:
Read the AMA response from Tuesday August 23rd, this addresses planetary motion and what they want to do, and the technical limitations of their options.
No Black Holes in Dual Universe, they could happen but they're not on the roadmap yet. That likely applies to other interstellar objects like Pulsars and and Supernovas.
Unknown if we can fly to stars or not. In the current system the stars are rotating around the planets, but they did say they want to make the planets rotate on their own so that may change.
Billions and Billions of planets could be a marketing thing for Dual Universe, but that's not really the point. They are more interested in having large populated worlds than they are giving everyone their own planet. So while there are trillions of star systems that could be procedurally generated, it will take quite a bit of time to actually get to those new systems (weeks to months for each system), so again it's not really the point of DU.
Ships are player made in Dual Universe, there's going to be an endless amount of variability in the designs that people make. Sure engine placement and physics may lead to some designs happening more frequently than others, but ultimately the market will determine what is a popular ship and what isn't.
Tracking "progress" in Dual Universe won't really be about tracking your progress towards a galactic waypoint (like the center of the galaxy or something). Progress is likely going to be measured in the same way that progress is measured in Eve Online. There's no "end game" to track your progress towards.
An AMA response indicated that we would be able to choose to fly to another star manually if we wanted, for several weeks or months, however the more common method of space exploration over long distances will be by sending unmanned probes to stars and warping to them when they arrive to build stargates. This is a pretty deep topic in Dual Universe, so I recommend reading about the game a bit to learn how it will work. It is nothing like No Man's Sky in that respect.
IIRC there are no ship to ship collisions in Dual Universe, however we've seen the demonstration videos which make it clear that you can fly your own ships (and do all sorts of manuevers with them).
If there's autopilot in DU, my guess is that it will have to be programmed by players in LUA. If you watch the 10 minute gameplay video from last month, you can tell he is manually landing his ship on the space station.
The trailer had asteroids and they didn't seem to pop in or out, and based on discussions in interviews about how the LOD system will work, it's pretty clear that we'll be able to see large objects from very far away. Popping issues are always going to be present when you're trying to balance LOD.
There are no NPC's in Dual Universe. If freighters aren't moving, it's because the owners aren't moving them.
Everything in DU is player made, if space stations start to look the same, blame the people building them, that's not on Novaquark.
There are no NPC's in Dual Universe. It's very likely all the planets will be somewhat untouched when they are discovered, so nothing should be littering them at all unless players have been there before.
There are no NPC's in Dual Universe.
Monoliths? This is Dual Universe not No Man's Sky.
Listen to the GrayStillPlays interview, there's a whole 5 minute discussion about biomes.
I don't think procedurally generating animals is a thing in Dual Universe. It's not even clear that animals will be in Alpha. Maybe someone else can correct me on that. It seems like Animals are going to be hand made, not randomly generated, but that's just my guess.
Watch the GrayStillPlays interview, again biomes and terrain are covered in that interview.
DU's skill system is time-based like Eve Online. Look at Eve's skill system, it's nothing like NMS in any way whatsoever.
We don't know anything about the UI yet.
DU is still in pre-alpha
The rest of your points could be summarized with, "This is not No Man's Sky".
Please watch this video, as it will clear up many misconceptions you may have about Dual Universe:
It's good to hear that most of these issues won't a problem in DU. I was going to get into NMS, but cancelled my pre-order and decided to take a "wait and see" approach to the game. I like EVE's skill system a lot and I also like that in DU we should be able to manually fly wherever we want. I also play Elite Dangerous (I know that isn't DU as well). But in my opinion Elite also failed to live up to the hype like NMS.
Initial Distribution will be stand-alone from any of the major PC Platforms.
After a time, who knows. It would be good for convenience sake to have it on Steam or GOG or something, but they've never really handled P2P games too well.