Here's an easy way to solve the problem for PC users (most mod users, assuming you have some tech aptitude).

Go to your (Hidden, Control Panel enabled 'Folder options') 'C:\Users\\Appdata\Local\Fallout4' folder. Make a shortcut and save a shortcut to that folder to save you future aggravation.

Locate the 'plugins.txt' file. This is the file the game will (so far, always) overwrite.

Launch your Mod manager program (I use 'Nexus Mod Manager', NMM). Activate all the mods and plugins you want (have they already been substantially changed with the latest patches? Are you sure you want to overwrite the default settings, now? Make a wise choice) .

Be sure the mods are also activated from the 'Plugins' Tab on NMM. Now exit NMM. Jump back to your "user\appdata" folder and locate the 'plugins.txt' file. Make a local copy. Mark your 'plugins.txt' file as 'read only' (Right click, properties). If you want to make ANY voluntary changes for your mods. Reverse that process before any updates. (Mark the file 'read/write', update mods, make a copy of 'plugins.txt', make it 'read only' again). Rinse and repeat as necessary.

Enjoy the universe in which YOU now reside.

Also launching using bilagos fallout 4 tweak tool totally bypasses this problem huzzah!!!