Vodyani faction is not affected by this - they can only ever have vodyani on all their arks/systems . Haven't checked the situation in which another faction invades an ark and captures vodyani population as non-primary population.

DESPITE THE MISLEADING UI MESSAGES : 'click to (spend this much luxury type Z amount) favor this population type, boosting its CHANCE to being selected when a new population emerges..' ; 'chance to increment: ' THERE IS NOTHING CHANCE BASED ABOUT IT.

On every system there are growth accumulator buckets associated with each population type present on that system. [NOT to be confused with the food accumulator bucket - typically of the size 300 food (1200 for vodyani) which decides when a new population is born/killed of via starvation]. Guardians (and I strongly suspect vodyani) get no such bucket. Primary race GETS THE GROWTH BUCKET EVEN WITH 0 of that population type currently present on a system. (you cannot stop the primary race from growing simply by exterminating them/sending them on spaceport endless trips. They still get to run in the growth race on all the empire's planets no matter what.)

All population types get 50 'growth units' to the growth bucket of their population type per turn. Slave populations in craver empire don't enjoy being slaves so their growth rate is slowed to +25 per turn.

Boosting with luxury doubles the bucket growth rate so +50 for slaves and +100 per turn for everybody else.

WHEN A NEW POPULATION UNIT IS PRODUCED (food accumulator bucket >= 300 food ) the game picks the population type with the highest current amount of accumulated 'growth units' in its population type growth bucket to grow when the food accumulator bucket gets >= 300 food again and RESETS to 0 that particular's population type growth bucket accumulator.
[I don't know how the game handles cases of equal amounts of 'growth units' for different population types except that the main population type wins every time if involved in the comparison]

There is a legitimate/exploitative way for the player to force a re-evaluation / election of what race type gets to grow next. PUT ALL THE MEMBERS OF THE CURRENT WINNER [doen't work with primary race since it gets to play even with 0 population currently on system but works for all other population types] IN SPACEPORT SLOTS - assuming spaceport present and that current to grow next winner has less members on system than your spaceport has slots. So when you remove all members of the winner population type the game is forced to set that race type's accumulator to zero and re-evaluate - chose another winner from the population types left on the system. A player can then bring them back from spaceport slots to system slots (the game doesn't set them back as winners - keeps their growth bucket set at 0 - THIS IS THE EXPLOIT) and can send the next winner to spaceport ... Repeat until the population type YOU WANT TO GROW IS THE WINNER .. You cannot use the spaceport to reset the growth of the primary race.

So max growth speed for primary race per system is 1 every turn at 300+ food surplus. [keep the system filled with primary race or keep the minor races under spaceport slots so you can reset their growth via spaceport]

Max growth speed for non-primary race per system is 1 every 2 turns (alternates with the main race) {keep all the extra population types bellow spaceport slot numbers so you can reset their growth via spaceport}. (as long as 300+ food surplus per turn luxuries boost doesn't matter since the one that grows gets reset to zero the other is above zero next turn ..). This is relevant for all factions trying to enable FIDS collection bonuses ASAP and also for horatio trying to grow minors to 2*N for splicing ..

More than 2 types of population in one system I would only use on purpose if I wanted to lower the growth rate of the main race (craver play) where the race type you want the least you get the most of ..

Example. 

Say you have 3 of a pop type and you need 12 for a horatio slice. [considering 300+ food surplus per turn systems ]

Send all 3 to 3 different systems that only have horatio (others less than spaceport) . Once they get there in two turns you get 3 + 3 = 6. Move 3 to different systems [travel time is hard to estimate but assuming instant] .. another 2 turns you grow 6 more and have 12. Ready to splice ..