Teach them that it's "situational." As you've stated, there are times where one fingering is needed over the other, but you should set a "default" and then find the variances from that default.
My preference is the thumb on the b-flat key.

I think the fingering charts use the b-natural key because "that's how it's always been."

Remember, orchestra's have been around a lot longer than bands. Orchestras play in keys that, mostly, utilize b-naturals so it was more common (necessary) for flutes to put their thumb on b-natural.