I have seen the same happen under the conditions you describe.
I rather would like to see a popup the moment my colonizer is cruising for a planet and said planet is taken by another, than have it keep on slogging on until it reaches its destination and only then pop up this (misleading) message. Currently a lot of turns (for said colonizer) are now wasted, possible even entire colonization opportunities because you will be (too) late giving the colonizer a different destination.