I unchecked read only just to see what the patch would do to the custom settings in the user.ini. Sure enough it reset them but no big deal, I had my old one saved. I assume the people that have the user.ini on read only when installing the patch will be fine.
Anyways I'm still not sure they are setting the right values in the user.ini depending on what you pick in the config options yourself. I was going to test it more but I said fuck it and just used my old custom config and set it back to read only.
One thing I did notice was before patch 1.2 even if I had my user.ini set to read only I could change the mouse sensitivity and music volume and it would save. After patch 1.2 it would no longer save these settings if the user.ini was read only. Just a heads up for anyone that is changing these and finding them resetting on you later.