Inbreeding! Assuming a pop represents a large number of people, it means that just one pop having the clone trait, you still have the problem of inbreeding. What happens when the previously recessive traits that wouldn't come about in a normal setting begin to rise up after maybe a few generations?
Well for starters, who said we'd only be using a single Adam and Eve pair to be the entirety of the clone populace? I was thinking more in line with
The Island or
Brave New World where the function is to create massive populations of viable pops, which is easily done with the ethics and technology available to Stellaris. This isn't hypothetical, the cloning vats are already in game, already producing millions of viable legions, already has technology to screen for and modify DNA at will, already has gene databases, selected lineages, even commercial gene modification available on a pop-wide level to the point where they can modify themselves, - assuming we did not clone from a diverse array of genetic stock, we could start with a single pair of Adam and Eves, clone them ad infinitum and subsequently modify their DNAs to create entirely new species or merely cause more genetic variation. That's just for human understandings of DNA, who knows how xenospecies work - it's ludicrous to say that my fungoid civilization is not allowed to clone itself in vats because of genetics,
when it reproduces asexually. Humans would only need a minimum of 80 clone pairs to found planet colonies from clone vats. Insectoid species, DNA modding species, plantoids and you get the point - could probably get away with far fewer, even just 1 pair. If my species is a strictly hierarchical genetically conformist but short lived beetle species for example, I would want to exaggerate their conformity, whilst any genetic diseases they would incur would be of no issue, as the drones would be infertile anyways.
Point being, it makes no sense.
On the assumption that a single pop is something like a billion actual people, a cloning facility that could pump out 1 clone per second would take 31 years to make a pop
If you made that assumption, however you could also make the assumption that each pop is 1 trillion people or it is exactly 1 person. Relevant:
It's been stated by the devs themselves that it's an abstracted figure with no direct conversion. The most likely interpretation, if you must make one, is that it's exponentially increasing like for example:
1: 50.000
2: 250.000
3: 1,25 million
And so on. The initial settlers will be more productive, like mining crews in Siberia, The outback of Australia and Northern Canada produce extreme amounts with a few tens of thousands of workers.
As population increases, more people will have more service oriented jobs.
Thus a normal human colony pod can be expected to contain 50,000 people, under this assumption. A clone legion is created by one cloning vat in 30 days, it is said in their description they reach adult maturity in
months and have natural lifespans of less than a decade. On this basis a science vessel could with its skeleton crew of scientists set up cloning vats on a planet and create the first pop shorter than the time it would take for the 50,000 in a normal human colony pod to set up. Combine that with gene screening technology, artificial life enhancement and a simple process of expansion (if one cloning vat factory can produce 10,000 elite soldiers in one month, soldiers that reach adult reproductive maturity in a matter of months (you know, cutting short 15 years of human puberty)), imagine what could be done with
two cloning vats. Then keep adding more and more cloning vats.
As it stands the spiritualists can crank out babies through the power of fiery fertile sermons. For everyone else, there remains no efficient, industrial ability to mass produce one's own citizens, despite all the technology for such mass production already being in the game. This is especially jarring for hive mind species who have no qualms with eradicating their neighbours and replacing them with their own species, yet balk at cloning vats for all except a military usage. I wish for there to be more depth to the gene modding :|