What is the in universe reason for pop growth slowing down as more pops are in the empire?

[Eladrin]

Increased (non-specified resource) overhead for a growing empire and demographic transition are probably some of the better in-game explanations.

While demographic transition wouldn't usually apply to gestalt empires, they could still be affected by the increased overhead for attending to a larger populace. Hive minds need to spend more attention dealing with infrastructural needs, and machine intelligences could start facing performance issues, needing to spend more assembly resources maintaining their population.

 

[Eladrin]

You could have applied a logistics growth curve to the empire as a whole, on top of the one you already apply on the planet level.

Each planet is growing slower as it fills up. But also the empire as a whole grows slower, as it fills up.

That's close to what we the systems do. Each additional colony increases growth since it's adding more production, but as the empire grows that additional growth is offset, generating another (mutated) S-curve. (We don't apply the penalties at the low parts of the curve since it felt pretty terrible in testing.)

There's also the assembly systems working alongside the logistic growth model.

"Boomer" is the game's true final boss.

It's clearly "Bubbles". Only a monster would name it "Boomer".