The mods that are permanent affect all saves made after that point, in that playthrough; it would not affect existing saves, or saves in a new game (though given the limited space allocated for saves on console, it would be better to start the game from a different PS4 account, if available, if you wanted to have multiple playthroughs going at the same time).
Yes, trophies will be disabled if any of the mods are enabled. There is a second warning about that if you confirm the warning about being unable to disable some mods.
