You can do it much longer before, but it has 3 drawbacks.
(1) (always) You cannot buy slots yet. More accurately, if you buy them, you'll lose them, and you'll have to rebuy-them.
(2) (rare) If you entered a game after the beginning, if it's one of the first route you create, you have a route image bonus, that will go down because you don't fly the route. Shouldn't happen often, and to most players not at all.
(3) (when you do it often) It clutters the assign route screen.
Does not prevent me from doing that, but forgetting to buy slots on flight assignment is a bummer, and happens to me sometimes. I'm checking regularly the "routes - view routes not being flown" screen to spot those.