Maps were extremely important back then. The various nations of Europe were competing for routes to India, China, Japan, the Spice Islands, etc. Spices were an EXTREMELY lucrative business. Some spices were literally worth more than gold ounce for ounce and pound for pound. The Dutch East India Company, the world's first international corporation, had many detailed maps of the world and kept them VERY secret. Accurate maps were highly sought and prized. Just a single accurate map could make a nation rich beyond its citizens wildest dreams. Maps caused wars.
The thing is, the real power behind nations were the cartographers. Without them, ships had nowhere to sail nor had any way to get back. Kings and govts had to make sure cartographers lived very comfortably because it one get fed up and fled to a rival nation, he took his knowledge with him. Govts must have spent a lot of time trying to entice cartographers from rival nations to defect to them with all sorts of outlandish promises.
But cartographers must have been, in themselves, a secret society. People are always jawing about Knights Templars and Freemasons and the Illuminati when the most secret society of all is under our very noses--the real kingmakers and deal-breakers--the cartographers. They had to have had a long line of succession and many older--far older--maps to use as source material. How else do we explain Waldseemuller's map? He could not have gotten his data from contemporary sailors. Here is a Spanish map from 1544, some 37 years after Waldseemuller's map based entirely on contemporary data:
Not very impressive. So we can surmise then that cartographers used old maps--mysteriously accurate--and added new info when it seemed to further refine their knowledge. The older maps were handed down or bequeathed to them by their teachers in the craft. Moreover, it seems likely that cartographers of even rival nations may have secretly shared maps and kept the most sensitive data completely secret even from their kings and queens. Sworn to secrecy among themselves, they revealed only what their secret society told them. To disregard that was to risk being expelled and this was a proud profession and none dared risk such a dishonor. Besides who knows what agents or other members this society had that could make someone die accidentally if they ordered it?
So we can surmise that Waldseemuller made a map that showed the isthmus of Panama six years before its discovery because he was allowed to or perhaps he did it without realizing the goof (pretending it was a goof). His subsequent maps did not show the isthmus and so it was either an agreed on one-time thing or he was made aware of his error by the society and told not to do it again. Scholars have tried to maintain that Waldseemuller was just guessing and got it right by coincidence but that is simply not very convincing.
There appears to have been a "secret" knowledge about the globe and the other stars and planets but where it came from is anyone's guess. For example, in Swift's
Gulliver's Travels he wrote of Mars as having two moons, gave surprisingly accurate distance of each moon from the planet and added that one moon orbited twice in a Martian day--all of which is correct but written 150 years before anyone supposedly knew that Mars even had moons at all. That Swift could have guessed this is beyond serious consideration. He got the knowledge from some source lost to us today but what was it and where is it now?