@Athinks I've sharing with you a save of my game. https://drive.google.com/open?id=19SURNzobjoyhFzSHbxhBUPFdth66fhqs .Your mode is active, but humans do not want to grow. Now only growing is Azizans race, they started from 4 pop, now there are tens. Humans do not grow a single pop sinse then. Even on home planet. The same problem I had with half humans : reverted to older save and forbbiden they growh. It is bahaving like for vanilia for me, and that is strange. 2.2.3 test_stelaris branch

As I was asked to provide details about pop growth wonkiness here rather then in comments, here it goes.
I managed to found a suitable point in my savegames to showcase the problem.
So, I'm running a two-species empire. One is founder with Arid preference, the other are primitives that I conquered less then 20 years into the game (they had 25 size world, I couldn't pass that). Founding species right now are Psionic, Conservationalist and Communal, while the 'cold' one are Very strong and Fleeting, so no traits that affect growth. I'm now 100 years into the game and there is 177-90 POPs disrtibution across 11 planets, 6 hot types, 4 cold types and one gaia.
Out of these 11 planets, 4 of them currently growing POPs with 25% habitablity. Two 'hot' have 'cold' species being born and vice versa. No migration treates, no refugee events. Reguees are welcomed, but these two species are living only in my own planets.
For the life of me can't figure out why this is happening. On average there are at least 2 free work and housing slots, amenities are above 10. Only one planet have a special modifier for POPs - 'Natural beaty' which gives +25% immigration pull modifier. And this is one of these 4 planets. Right now there is one planet with low stability, but this issue was going on for a loong time in terms of game progression.
I have Glavious AI, plus a buch of UI modifications. 2.2.3, 1960 version of the game. All major DLCs are here, except for Distant Stars story pack, I think Savegame is here https://drive.google.com/file/d/1QOZN5bk5xcwMHDcFWVmH9A92RJs6uqd2/view?usp=sharing

Thanks ShaTiK. And thank you for such a detailed post. It really helps with the debugging. If I have time I'll look at the savegame tomorrow (although fairly busy atm).

The ratio of pops sounds roughly right (going off standard starting numbers and amount of years elapsed). Migration + the tiny bonus of underrepresentation is likely causing the growth, although honestly it probably would happen with 0 underrepresentation and migration. Having the species on the other planets means they can be "pushed" to others.

I think I'm going to look at increasing the habitability modifier to 100%, so that anything below that starts to get maluses to being picked, but I'll have to test it. I might also tweak down the underrepresentation modifier even further (as that seems to outweigh hab and popnumber stuff sometimes), but the problem with removing so is that it makes runaway growth of a single species almost inevitable as soon as they get even a slight number disadvantage on a planet, and then on other planets (so it causes a different set of habitability related problems).

Having messed around with these numbers, I really wish pop growth and pop migration were two different systems, rather than being lumped together by weighting. It causes a lot of problems like those you mention.

Originally posted by Athinks:

Having messed around with these numbers, I really wish pop growth and pop migration were two different systems, rather than being lumped together by weighting. It causes a lot of problems like those you mention.

I think devs went too ham on this 'balanced' representation thing. It's one case when you have 50% habitability pop growing when 100% habiability pop could grow - that I can understand and accept. But 20% vs 80% - and these pricks keep getting grown? Nah, screw that nonsence. I get that some pop could be crazy and live in totally unsuitable conditions. It would be a few percent from the total planet population, around 5 I would gess. So for every 100 pops 5 could be of ill-suited habitability, that's plausible to a degree. Still stupid, but fine, paying increased upkeep for these 5 pops is not a big deal. But 20% of the planet pop are the same crazies? No way

Yeah. A small proportion makes sense as people do live in uninhabitable environments sometimes, for different reasons. And underrepresentation works really well if you wanna RP/play a really varied and multi-species empire without having to worry about it too much. Unfortunately now knowing the exact formula for underrepresentation weighting it is hard to work out how to get the desirable ratio. As I say, I'll have a fiddle.

Originally posted by Athinks:

Yeah. A small proportion makes sense as people do live in uninhabitable environments sometimes, for different reasons. And underrepresentation works really well if you wanna RP/play a really varied and multi-species empire without having to worry about it too much. Unfortunately now knowing the exact formula for underrepresentation weighting it is hard to work out how to get the desirable ratio. As I say, I'll have a fiddle.

Thanks. Chances are devs would tweak the numbers in the next few patches. But then again, they have to fix terrible performace and abysmal AI first, so things like POP weighs could be down the list. So your mod, as well as Glavious AI, still would essential to the game in the neares future, even after a few patches. 'Cause at lest mods could fix these things, no mod could save performance from tanking due to, likely, some amazingly inefficient calculations on part off the game itself