I'm not sure what's so confusing about the WNM costing more than The Cage.
When The Cage was made, literally everything had to be built from scratch. When WNM was filmed, 90% of the sets were reused, costumes were reused, the model of the Enterprise was reused, effects shots were reused, etc. They had a ton of savings in being able to use elements that were created for The Cage. That's the reason why the episode costs so much less.