IhromantMod usually improves the speed of the game. From the speed standpoint, when you missed to include Fresh Mod, you will receive ordinary Wywerns and Angels in conservatories. So, It could reduce your speed of acquiring battle stack and slow your speed down. My assumption would be for now that there will be continuation of the game.
Also you can't predict which castle pair it would be before joining. So if you forgot to on Fresh mod, you can stuck in the situation with 3 hives on respawn and strong GO. In case with Efreeti, it's painful, but still possible to break it, but with unupgraded wywerns - it's a complete disaster. The only castle is weakened with Fresh Mod are Necro and Conflux, so low probability to get them.

TL;DR. I'm considering 1st variant for now.

If the tournament is conducted with Fresh Mode, its quite strange to say that the game that was started without Mode should be continued. What shall the player do in the situation when his opponent asks him about being a host and after that creates the game with the Mode being turned off? Especially if this opponent voted about Fresh Mode being not used in the tournament. Your answer about the proposed situation got me thinking that your rules can be abused. Its kinda bad situation in terms of principles of fair play. I think your rules should be more striсt and enlightened in terms of prevention obvious abuse.
Actually i liked the idea of kamukag3e. Im sure it should be taken into consideration.
And i dIsagree a little bit about the statement what towns had been weakened with Fresh Mode. I would rather believe that Dungeon was kinda nerfed with this mode not only Conflux. I remember recent times when u couldn't pick the hero for Conflux on Jebus-Cross. This town had been rather averege. With permission of picking Luna on the start Conflux became the way stronger. But i should say that not all the games by Conflux is determined by Luna's success with Angels. Necro is nerfed substantively ofcourse. No shit. But this mode is interesting for me especially in terms of improvement the tempo of Tower and Stronghold on Jebus-Cross template. These two towns should become stronger as well. Im wondering what the balance will be. And we gonna find out it with the help of Fresh Mode and This Tournament!