These are Limos class worlds with alien life forced with setting, right?
No, none of the worlds I posted above are Limos. Siwa and Medusa (but I couldn't determine which is which now).
I do suspect that the world type choice short-circuits rolls. It may force results, where the data created in previous world building steps is ignored in favor of some templated standard.
That would be fine if it was deterministic throughout each step of world building process, but it appears not to be or not working as such.
Excuse me, I got bit confused when you cross posted a link here in the other thread, I see now it wasn't really relevant question.
Overall, I don't really see anything out of order in what you posted. I have observed that the game does seem to make hidden rolls of sort (or perhaps fetches some basic template and then does variations on it, never staying too far). One that particularly sticks to mind are the biosphere colour variations on Medusa class. There are at least four of them (yellowish green, bluish green, cyan, red) but by the time you get to biosphere generation the generator is often hellbent on giving a particular one to you, usually either of the former two.
To comment on your initial posts in this thread in order:
1) This is bit weirdly indicated, but it just means the plants don't die due to atmosphere. They'll still die because the hostile alien bioshere.
2) This just means density/pressure. Bigger planets tend to have higher pressure.
3) Insidious, deadly* and zero value seems enforced for Medusa. The farming hazard rarely goes up, and if it does it seems to be due to lot of CO2. With billion year life history you probably have fairly young planet so you are more likely to get more basic vegetation (youth also seems to increase possibility of aquatic only fauna, provided you have lot of water).
4) No comment.
5) Water does seem to have some kind of hidden roll, but I have also had more luck with both water and rainfall on hotter planets. The terminology "arid planet" is weird, and should probably be understood in relation to Earth with 2/3 water. It's just that the game doesn't go more wet than arid planet at the moment (due to lack of navies presumably).
Geological activity at least presumably has some environmental (e.g. age, planet class) factors to it.
6) Same as 3.
*BTW, deadly in combination with non-zero value is bit weird, because it doesn't prevent xeno farming, not sure if this is a bug or if the idea is that some basic treatment can detoxify the crops.
demiare, yeah does seem fixed now.