What exactly needs to be done to keep system preferences from defaulting back to on?

I have this constant irk with system preferences re-enabling themselves in the background. There are three that keep turning back on regardless of how many times I disable them.

• The Gatekeeper setting to prevent using apps that didn't come from Apple
• The "Magic Quotes" text setting, which replaces the standard single quote(') and double quote(") with curly versions.
• The "swipe between pages" behavior of the trackpad

Some context: I am a programmer, and these behaviors routinely destroy my workflow. My laptop is not a tablet or a phone and I do not want it to behave like one. The gatekeeper setting prevents me from running my own programs that I wrote. The magic quotes setting routinely destroys my apache and nginx config files. The swipe between pages setting routinely causes page loads for stuff I am working on that runs for a huge amount of time to reload before finishing. I have disabled these god knows how many times, and have also written custom info.plist files to permanently disable the behavior, but they still turn back on every time a system update runs. It simply ignores my settings and the system config I have written and turns them back on anyways. This occurs pretty much every time I update the OS, and causes about 3-6 hours of fixing broken things and tinkering under the hood to see what it broke and turn it back off every single time an update runs.

The purpose of the info.plist files is to override behavior exactly like this, and those do not prevent it from re-enabling either. The update simply ignores them and/or bypasses them. I did manage to get Gatekeeper to stay off instead of resetting every three weeks or months or whatever the default is, but it does still re-enable whenever an update takes place, leading to having to do this stupid little dance to get the system to recognize it again and reboot multiple times just to get it back to what it was already set up to do. Similar issues occur with the other two settings.

There needs to be some way to designate in whatever fashion, either technical or through the OS, that settings I have intentionally set DO NOT CHANGE FOR ANY REASON.

Thanks in advance.

PS: Please give a good slap in the teeth to whoever thought that making a plaintext editor auto-format text was a good idea. We have Pages for that stuff. Plaintext editing means, well, plaintext. As in TYPE EXACTLY WHAT I WROTE AND DON'T MAKE ASSUMPTIONS ABOUT IT. If I have a typo, that's on me. DO NOT AUTOCORRECT IT IN A PLAINTEXT EDITOR. Do not change my verbage, spelling, character syntax or any other thing in a plaintext file. Currently, I have to turn this behavior off in three different places just to get it to stop doing that, and all of those routinely reset to back on with no particular rhyme or reason for doing so.