Ok, so I went the extra mile here and did some trouble-shooting, dropping a save game before i started using an excessive amount of console commands. Warped to every sector in the system and here's what i found:

Looked like all the starter planets (for me that was Akua, Tallodar, Haven, Gaia, and Persephone) all had the same items below (in orbit, didn't go down to planet):
- Polaris Mining Facility
- Pirates Hidden Station
- Bunch of Zirax and Asteriods

What they all were MISSING:
- Orbital Trade Station
- Distillery
- Club Inferno

I was able to start the mission by using the console command "pda brief 004" and was able to complete it only by clicking off all the boxes as they came up. This skipped the mission essentially but gave me the reward. I was then able to continue with the next vanilla mission just fine (Titan had spawned properly and I noticed the other main POI's that are mission related to the vanilla story in the starter system were there).

So in short, the missing spawns seem to be the problem. Less of a problem seems to be that the things that are there are in every starting planet (more of a duplication thing which isn't a huge deal I suppose).

Not a huge issue for me since I've been through vanilla at least once and am just going through the story missions again because it's an easy progression loop and some of them are pretty fun. But until a complete fix is in place other users can use the workaround I used to at least continue on, skipping the "mission 3" vanilla mission (actually mission 4 because the game counts prelude as mission 1, but you get the idea).

Either way, enjoying the scenario so far and I hope to finally get into it properly once I have something warp-ready (without cheating this time)!

I see the problem.
Will be fixed next update.

The update is for new save ?

Originally posted by zarvoxbe:

The update is for new save ?

Yes it would require a new save sadly.