Geoff the Medio wrote:
This makes building colony ships a quick way to generate poulation units, and could become a serious balance issue in future if there is migration of population between planets or the ability to unload colonists from a colony ship to an existing colony.
It seems like the ability to "unload colonists from a colony ship to an existing colony" is the much more problematic part of the two listed above. But really i don't see why we need to be able to do that. It seems to be contrary to the earlier embraced design idea that we won't be manually shuffling population around.

Simply declare it impossible to "unload colonists from a colony ship to an existing colony" and most of the problem goes away.
But still, "where do the colony ship population come from?" is a valid question.
Geoff the Medio wrote:
The "simplest" solution is to deduct the appropriate number of population from a planet when it builds a colony ship. ...
Whoa, sounds like you've forgotten about
shipyards. With all ships built in a fraction of your total planets, subtracting population only from the building planet would be a problematic hardship for shipyard worlds.
The other aspect to consider is the species of the colonists. Though it's not clear if we would want to require a shipyard on a species X planet, to create a species X colony ship, or if we would allow any shipyard to build a colonyship for any of your member species. Another possibility is that colonyships are species-neutral, and you get to define it when you plant a colony. I don't think we can choose how the species aspect will work at this point, but we should be aware that there will be more to colonyships in the future.
I would advise that we stick to the current unexplained generation of 1 population unit, until the point that it becomes clear there is an un-resolvable balance issue with it. As you point out there are a number of complications involved with actually taking the population from somewhere. I don't want to wait for the population bar to fill up, and i don't want additional resource type requirements in the production queue if at all possible. Also, i don't see what the problem is with "sudden loss of population on the planet(s).", as long as we don't let it kill a colony. In the case of population boarding a colonyship, sudden loss of population is what you would expect.
Geoff the Medio wrote:
This type of system could be modified later if and when we set up a migration system between planets. Population wanting to migrate off a planet could perhaps contribute to the colony ship population, even if the planet isn't able to produce more population by growth.
Once we do get a auto-migration system in place we'll have some better options to make it fancier, if necessary. But it's not clear to me that fancier is at all neccesary.