Number lines are never meant to be taken as “drawn to scale”. Expecting them to be equal in length because they represent the same physical length is a common mistake, but it’s still a mistake.
You can't compare two fractions on two number lines unless they are exactly the same scale and perfectly partitioned.
Try using a number line to determine which is greater 5/9 or 9/16.
That's really the point; you can use a number line to demonstrate the process, but mandating that the kids use the number line to solve the problem will only confuse them.