Yes everything should be at the correct scale (or most of the zone lines wouldn't match up).
It's interesting how some zones have quite a bit of the connecting zone attached to it, like Nek/Lava for example. They obviously put some of the connecting zone there to give the illusion that the zones are connected when zoning, but some of it seems unnecessary.
Lavastorm/Nektulos
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Lavastorm Selected
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Lavastorm moved up on the Z Axis
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Also if I was to scale Rathe Mountains up you can see that the zone lines are out of scale.
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You could scale the other zones but you would mostly just come back to where you started but with everything just bigger.