Earlier quoted context omitted.
I think you are conflating people calling the Trojan war fiction with thinking the city was. While there were a few people like Bryant who thought Troy was totally fictional it was always a very fringe position.
What are you talking about? Here is the Blaise Pascal quote in the first link: > "nobody supposes that Troy and Agamemnon existed any more than the apples of the Hesperides. [Homer] had no intention to write history, but only to amuse us."
I think you are confusing people debating the historicity of the Trojan war and the debate on the exact location of the ancient city with people thinking Troy was thought to be fictional and rediscovered. The latter never happened and people using it to imply Atlantis might exist are using the debunking of one conspiracy theory to prove another one. This is like using the Moon Landing being real to prove Roswell.
Edit: Troy, generally being referred to as Ilium (where we get the Iliad), or Troas is in the Acts of the Apostles as a place Paul went, it had a bishop who attended Church councils, it was part of the Roman empire, you can buy coins from there today https://www.coinarchives.com/a/results.php?search=ilium this is not at all comparable to Atlantis.