As I explained in the post immediately above yours: You make changes like you would always have: You edit the skyrim.ini file.
But you absolutely must not delete the .base or .baked files, just ignore them. And you must not set any of the files write protected.
Vortex will import the changes you made in the ini file back to the other ini files automatically. Everything should work like it would if you used a different mod manager or none at all.
Sounds great, but then why is Vortex reverting any changes I do to the .ini-files as soon as I click deploy mods? Doesn't matter whether I make the changes in-game or with the config tools or BethINI, or editing the file in Notepad. If I turn the music off and invert the mouse y-axis in game, Vortex will have reset them the next time I load the game if I have clicked deploy mods in between.
It shouldn't, that's what I said before. If this is what's happening then report it as a bug.
(Also, why is Vortex asking me to deploy mods every time I start the game even if I come straight from deploying mods in the mods section??)
Because Vortex can't know if anything changed that requires re-deployment. You could have edited a mod file outside vortex or the ini files. The act of automatically
checking if deployment is neccessary would take almost as long as deployment itself so it would be pointless. If you don't want to be asked, just enable automatic deployment
which is the default setting anyway.
How can I edit the ini-files in a way that Vortex accepts? What file should I edit if I need to change the Fallout4.ini settings?
Again: you edit fallout4.ini like you always have and you don't do anything you wouldn't do without vortex (like deleting files)
Is there a way to revert any problems I may have caused by deleting the said files?
Only thing you can do is close vortex, delete base and baked again and then edit the ini file manually and return it, from memory, to the state it was in originally.
If you happen to not have memorized all ini settings you can only delete the file and start the game, so they get reset to defaults.