Hrmm... I suppose the heart of the issue lies in that there really hasn't been this sort of situation before. Sky terrain is generally illogical, as very few maps are set in a place where there is a castle on a cloud. Chasms and other such cataclysmic events where there are fissures in the earth are more likely.
But I am going to hold firm on that they should be able to levitate the gap.
Here's how I see levitation: You have three basic types.
Brand A: The Link Archetype when he uses the hover boots. This is ideally how I imagine Mages using levitate, walking on air for a short time, then dropping. They can't go above anything, they just float above it. Cliffs still cause them pause, as they cannot magically walk over them.
Brand B: The "Floater" Archetype. They are constantly inches off the ground, usually as a mark of their magical superiority. They never leave the ground and plummet immediately when over a surface that isn't solid. If you are familiar with Kingdom Hearts, Sora's Final form is fond of this.
Brand C: The "I'm a witch" Archetype: Not content with Brand A or B, these characters defy gravity and spit down it's neck. They float around of their own volition like a nymph. Neither mountains nor valleys give them pause. Usually immaterial anyways like a ghost, so this makes sense.
Now, obviously Fire Emblem Mages are not of Brand C. That would be silly. However, so would them being of Brand B.
It's hard to imagine that the second they get into a combat zone that they would decide to suddenly start levitating. Regardless of the circumstance. That would require a gross misuse of magic sustained for a longer period of time than is reasonable. If you are focusing on floating in the air or suspended; you are a target. You are right in saying that they can't just ignore terrain. If in the current chapter of the Noble Emblem 2, I fully expect Colt to have to take a penalty when walking in the swamp. He may be able to move from place to place easier, but he can't sustain a levitation spell and fight at the same time. So he'll have to take the -10 to HIT and EVD.
That is why I think they can bridge the gap. They aren't constantly floating over the ground as suggested, rather they are using a technique similar to Brand A. They use tactical levitation to get across a gap, because they have limits. They cannot fly, this is true. But they can cross across something as if there is an even surface, if only for a time.