I'm picturing the number of messages they'd receive the day the update hit. People suck. Most will understand that they need to hold off on updating if they want to play the mod, some will seek support when it breaks. Some of those will say "that makes sense" and disappointedly wait for the mod to update, some of those will get angry. I certainly wouldn't want an inevitable flood of angry emails a few days after the big release.
Yup, if you use mods, it's a good idea to set the game to update on launch through the game's properties menu in its steam library listing.
Since a F4SE nodded game is going to launch through the script extender's launcher, that keeps the game from updating automatically when starting a play session.
I also like to make a copy of my game folder and save it off in another drive so I have a backup.