Benevolent traits, brindle's observatory, and the hidden alien base event generate colony ships or planets with 5 population.

This is apparently intentional to make them useful, but civilizations that put 5 billion citizens in 3 billion cap planets and kill 2 billion of them do NOT feel appropriately benevolent.

You can transfer population with colony ships but it requires incredibly awkward micromanagement and delays the ability to activate the ideology.  AFAIK Benevolent + prolific actually makes the minimum starting population over 3.  To avoid "genocide" you would theoretically need a fleet of standby colony ships while you construct tier 2 capitals.

There must be a less clunky way.

Instead of providing bonus production on crowded planets with a population drain, what if the extra population stuck around but simply provided no production?  You would still be motivated to move the "unemployed" to reduce the morale penalty.

Additional note: the traits which add bonus planetary tiles in the benevolent and malevolent paths would be better implemented as terraforming improvements instead of a random tile which is frustrating, encourages savescum, and is not conducive to well planned colonies.