From my testing the transports are built without troops. I have been parking them in nearest planet (Altaria) and popping them back out next turn. At that point I do get the slider asking how many to place on the transport. I am getting enormous odds on invasions 175 to 11, Even on planets with 22 billion.

I am not 100% certain how the Colony Ships generate but once constructed, their initial contained population should degrade significantly the farther it is away it is from the main sponsor planet. Colony Ships constructed in deep space should start with a ridiculously bare bones amount of colonists. The world is claimed - but more people need to arrive from elsewhere or the production is going to be sloooooowwwww.

With this said, it seems new worlds should 'call' more colonists to the new planet from the nearest highly populated worlds in the form of population routes set up by the player (similar to trade routes). Colonist Transports/Liners (not Colony Ships as the colony is already settled) should then travel along these routes to populate the world automatically above and beyond the new planet's growing native population. The idea of them being magically transported is something I am not comfortable with. But again I am not sure how it is actually happening in game at the moment.

similarly colony ships always launch with 2.5 regardless of what you set the slider to