I somehow never really noticed and have 1500+ hours in VP. Guess something new we learn every day.Pretty sure its been that way for a long time or maybe even forever. You normally don't get pop bonuses twice (whether its progress, the authority bonus on pop, universities, etc)
Regarding the bug .. It seems to not happen on windows. But the linux version is breaking pretty frequently. Anyone running VP 3.3+ on linux with proton-experimental? I prefer not to login to windows for playing VP
Finally .. this version is significantly harder for peaceful play. I am significantly behind in science even with a progress start on deity. Pretty much down by 10 techs in first 60 turns. Turn 29 - 33 statue of Zeus is gone. 55-60 Terracota. Other than stonehenge/pyramids with a good starting location, pretty much impossible to build any wonders until industrial era.