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.
Thank you. That is what I was afraid of.
I mean, disabling trophies while mods are on I can see and understand since its been a thing in games for a while, but the part about them providing you said mods and making some of them permanent seems like an oversight or at the very least an odd choice all things considered because then it discourages using the "presents" they are giving us if we care at all about the trophies, since activating them will bar us from ever even trying for them in the future. Odd they wouldn't be able to be toggled on/off just in case you forget to take them off while making a new file, since being on the game menu I assume means it remembers its on even if you exit game.
Oh well, guess I won't get to test them out for a long time since I'm still halfway through the honor run and my play time is limited