To my knowledge, making a Species Mod more compatible is actually ridiculously easy. Go into each of the Vanilla files and move the code you added out of it and into its own text file, formatted the same way as the Vanilla rendition documents. I know for a fact that planet classes are completely compatible this way. Your Stale Worlds should be in their own file. You can also put your custom Civics in their own files.

If you put your Trolls in their own class (make sure you keep the BIOLOGICAL entry in it) in their own file, separate from Mammal/Avian/etc., you can also make them universally compatible with every Mod that exists.

Unfortunately, the Citizenship Types, to my knowledge, cannot be separated. Since you created a new Citizenship Type AND applied that to Vanilla rendition Jobs, you are screwed on that regards.

I have no idea how to make Mods for "Stellaris", but I know enough about the organizational structure of Paradox code in general to undertsand this. Indeed, I have seen other Mods use this exact method to add new species. The game will count them as Biological if you set it accordingly.

If you are concerned about file size, remember that bloating the Mod for the sake of compatibility is not bad thing. Besides, adding one megabyte to the Mod is not bloating. All of the compatibility stuff I've suggested is done in text files, which contributes little to the size of the Mod. If it can fit on a floppy disk, it's nothing.

IMO, unles it's a total overhaul or a graphics improvement Mod, your average Mod should not exceed ten megabytes.

I can confirm the new Stale World planet class and the Desolate Origins civic have no compatibility issues currently. I have shifted the Trolls into a new species class, Insectoid, with biological attributes included, and a new graphical culture using avian_01 as fallback.

Yeah, I am aware that citizenship_types, species_controls, start_of_game_effects, and scripted_triggers_jobs are unable to be separated. Unfortunately, these values are needed in order for the Hemospectrum civic (which is supposed to work similarly to the Syncretic Evolution civic, hence why its code is so similar) to function as intended. This is leaving me to consider axing the Hemospectrum civic entirely, and find out another way to reflect these changes without using the civic.

1. I suggest you name the separate class for the Trolls something besides "Insectoid", because that would override the deafult Insectoid Species Class. Just list the special Species Class for it as "Troll" or "Hemo-Spectrum" and "TOLL_SPECIES_CLASS" in the code.

2. If "Stellaris" code is like CK2 code, then Start-of-Game Effects CAN be separate files. You will need to write them into a new Event AND create an entirely new On-Action file. Use the trigger for that Event at the game's start. You can create new On-Actions using the same triggers and "pulses" as the Vanilla rendition, and "Stellaris" will know to fire them in alphabetical order using the name of the each TXT file.

3. The Hemo-Spectrum Civic has to replace stuff. Sadly, if it's adding Citizenship Types and the like, it can't be added on. Perhaps there is a way to write a Policy for it and use Events to prohibit different creatures from ruling?

Is it just a problem with me or is the Hemospectrum civic bugged with the 3.8 update, because all trolls started as sea dwellers for me instead of the intended result of having 3 separate subspecies
I have tried turning off every other mod (which are just Tiny Outlines and UI Overhaul Dynamic) and the same result still happened
So is uninstalling and reinstalling the mod
And rolling back to 3.8.2 and 3.8.3 (the current version is 3.8.4)

Unfortunately, I can't seem to reproduce what you're experiencing. Everything is behaving as intended on my end, so I have no idea where to begin in fixing your issue. Are you able to pull up the error.log and find anything in it that might be causing this?

A species I ran into has the sea-dweller trait, which meant they could only take ruler positions. They did not have other species for a hemospectrum, just them as a bunch of unemployed pops.

i started a new game and the condesce didn't spawn with the immortal ruling caste trait, but their heir did and i can't seem to add it with commands

3.12 did break the portraits, its a few file changes on your end but you have to update for it to work

if the AI ends up spawning with this civic they stop working since the other two pop variants don't spawn