What was the difference?
There was none! The environment that Mary Queen of Scots experienced is quite the same compared to the environment leading up to the development of the Vigenère cipher. In fact, it even states in the book that Vigenère’s publication of Traicté des chiffres happened “ironically… [in] the same year that Thomas Phelippes was breaking the cipher of Mary Queen of Scots.”
Even Mary herself was aware of how insecure the code was. It was just that (1) she could not come up with a better method of encryption and (2) she never questioned if her beloved messenger was a double-agent for Thomas Phelippes which he in fact was.
All of this just goes to show how much of an edge the cryptanalyst had over the cryptographers. No matter how much variation the cryptographers tried to invest into their monoalphabetic, the cryptanalyst could break them easily with one tool — frequency analysis.
However, this was only until Vigenère took the works of three other men to create a cipher that gave the edge back to cryptographers. With it, cryptanalyst would be left to sit hunch-back over their desk for years. It is only a shame however that his amazing cipher would not be appreciated until another two hundred years.