i know i am new to the forum, but i am not new to the game.
In my opionion it would make many senses to ignore any scripted/moded/improved lua files or whatever ( i have no idea of the current technical status of mods right now) as long as the game is starting.
I might not know about modding Factorio but programming in general is not that much of a secret. I am a steam user, i know, but i don't care, i still found this gem and want to enjoy it.
Most Mod Programmers take not the least care, it took me 4 hours today to get back a working version of the game on my computer, because you are incompetent. I know this is harsh, but you were not aware
of your responsibilites here. Anyway thank you for your efforts. Now back to the developer, how about the game launching and ignoring any non-vanilla content ? Not working, engine not ready ? Well make the engine simply restart after installing mods, nobody would mind, thats normal. And protects people from a major hassle because you integrated mods into the base of the game, so anything that does not work because of incompetence of Modders, keeps them from enjoying your game. The Game, for no reason, accepts changes to its most core defines and inits. I know this is very appealing to modders, but keep the above in mind, they wished they were as good as you are, they wished to create an original game, like you did, but they did not. So please make your game bootable, no matter what changes some alzheimer modder made forgetting to add some file his scripts rerfered to.
Mods have killed my Game seriously, it took me quite some time to delete all leftovers. I know you put lots of effort in creating them, but you failed and a warning is nothing that keeps people from using them, just keeps them, well, warned. They still will have to manage the cleanup all on their own, so your warning is for the trash bin. It might even fall back on the game, so great job you damaged the game you wanted people to like even more.
Basically i would appreciate the developers to establish some core that allows us to boot the game without any mods, any time, to use the in Game Mod Manager, which is most likely a good repelant, to keep incompetent Mod Makers at bay. So i can at least uninstall their BS.
I know this sounds hard for Mod makers, but it is partially a structural problem. Don't let imbeciles mess with your code

-DM_