I think there is a connection here - when the growth slowdown kicks in depends a lot on habitability and galaxy size. So a mechanic feels a tad restrictive on low habitability feels much much tougher on higher habitability.
I am sympathetic to people who think they should have cut the base number of pops per planet and adjusted from there. As you say, it’s an abstraction, so having fewer or more pops doesn’t really change anything.
Having the population growth rate decrease with empire size I feel is just a bad mechanic, because it doesn’t make sense. It’s hard to see why you could say triple the growth rate of a set of planets by dividing them into 3 closely-allied empires versus one empire. It doesn’t seem like the implications for some types of empires that can’t conquer pops were thought through.