The way I always thought about FO handling massive empires (which is, after all, the point) is that you're unashamedly 'Imperial' -- that is, you're going around conquering and colonizing. A colony, by definition, is an extension of the 'mother' Empire. For the purposes of the game, 'race' really refers to 'species plus culture.' There's not really a modern-day analogy because we haven't seen any real, unaplogetic Empires since most of them collapsed in the early 20th century.
At any rate, a colony ship should probably require a negligible piece of the parent colony. I'd say that there should be a minimum population requirement to create one -- not very high, necessarily, but you don't want to be making colonists from a brand new baby colony -- and that the ship should not actually eat up a population point (or should eat up a small fraction of one such that you wouldn't notice it unless you made a whole bunch).
As far as multiple races per planet are concerned, I vaguely recall that we eventually wanted a model for this, but it would be covered by an immigration/emigration system and not by colony ships. Colonies should always be ze motherland. Anyone else can fly their on their OWN ship.
Well that depends on how we want population+races to work.
A planet becomes part of your empire in one of 2 ways
Now which of those can give a different race from your starting race depends.
option 1.. Pure Race= Xenocide is the only option in conquest (MOO1)
option 2...Natives= Conquered planets may retain their population, but that population can't colonize or be moved to other planets in your empire
option 3...Multiracial colonization=Races can be moved off of the conquered world in colony ships
option 4...Multiracial Imperial population movement=A planet can have its race changed from one race to another even after it has been colonized.
option 5...Multiracial worlds=A planet can have a population of multiple races (MOO2..although it lacked option 3 which made it require micromanagement)
I definitely don't want Option 1,
Option 2 seems unusually limiting.... I want race X on a planet, so I will wait until the Race X empire colonizes it and then conquer it.
Option 3 seems like a good compromise position... some micro is involved (must wait to colonize until I have Race X available... but once I do, I am more flexible with it.)
Option 4 Could work, as long as the system doesn't involve too much management, and enough cost, ie it takes time to change over.. possibly time in which the planet is unproductive.
Option 5 involves too much "fiddling"
As a side note, the reason we don't have any modern concepts of "race" as species plus culture is that we only have one species.
I imagine if the British Empire had discovered easy interstellar travel in 1900, say, and it claimed an Earthlike planet, then they would settle population from India in tropical regions and population from Egypt/Australia in desert regions. Those populations might have no more political power than in their original place, and they might not even be loyal (ie Australia/America were dumping grounds).. there might be some white overlords, but the key thing would be that the Government would be British. And if the British conquered an inhabited Venus/Mars/Jupiter-like Planet, you can bet they would use those people to work their colonies on Venus/Mars/Jupiter.
The way I see it
Colonization= Conquest of 'land' and then fill it in with whatever population you want for that 'land' to actually make it productive.