if they are autoflowers, it is irrelevant.. do what is convenient. If it's a photoperiod, you should do this during light cycle, because interrupting a the dark cycle will potentially fuck things up.
common sense otherwise.. make sure they don't topple over from normal forces of being in a moving vehicle. Moving truck? or if vertical height is a problem yo'll have to lay them down.. if moist enough, should reduce how much medium falls out. AGain, can rig something up as a temporary cap that holds everything in place, too.
It's just a plant. apply common sense. don't let sticky buds touch fuzzy or fiberous things. maybe a garbage bag over the top of the plant if not too wide.. or just some plastic protecting it from picking up threads and debris from anything else nearby.