This is already being done by the S-curve growth mechanic, so the penalty per pop in the empire mechanic is essentially superfluous. I see no reason not to just remove it. Planets already naturally peter out in growth as they become populated.
If you have "breeder planets" that don't have jobs, the pops will migrate to your more populated planets. The logistic curve on purely a planetary basis would do almost nothing to reduce endgame population counts.
In many of my recent playthroughs I've got some developed planets and a number of semi-developed resource planets. The pops that grow on those resource planets move from their rural backwater over to get jobs in the big city, eerily simulating urbanization. (Unemployed pops will almost always move to the planet with the most available jobs.)