Once per pop-group per planet, not once per planet.
The assumption is that there will be fewer 4.0 pop-groups than 3.x pops, but that's an untested assumption.
Given how 3.x AIs routinely generate 10+ versions of each species, in a galaxy with 20 species there could easily be 200 sub-species, times 4 ascensions, times 8 ethics, times 3 stratum (or 4 stratum). That sums up to more possible combos on one colony in 4.0 than I have individual pops in my whole empire most 3.x games (19,200).
And 20 starting species is not a lot.