No, I'm going to allow removing toxic atmosphere on volcanic planets or extreme weather on gas giants. Other planet types can remove it or suppress it with Domed Cities.
I've addressed the defense penalty on Domed Cities many times before this thread - ultimately I decided not to add a settings option to remove it.
Can you post a screenshot of the organics problem with the water world? I think it should be possible to increase them there.
Lobster seeding time is controlled via the settings file. If it happened instantly, you may have set the time to 1 day.
It seems like you really want to customize the mod even more than the settings file permits - I would recommend checking out the source code (https://github.com/boggled-starsector/boggled_modpack/blob/master/TASC-Source.zip) and making changes to it to fit exactly what you want. Removing the defense penalty on Domed Cities should be trivial.
For the toxic, weather and defence fair enough.
For the organics and lobster, I forgot I hadn't actually changed it to a water world yet, I just named it Water World, after the movie, naturally it's got extreme cold, yeah my system looked so nice when I picked it.. near the core, good ores/volatiles, which fitted my miner run to a T. Alas I ignored all the conditions. -sigh- Still, it's been an interesting learnin experience.
As for editing the mod, that's a tad out of my area of expertise.
My main aim from all this was just handing out ideas/suggestions, and attempting to point out bugs, though the bugs turned out to be user error.
I do have one last suggestion, perhaps allow AI cores on the buildings for the demand and upkeep bonus's?