My current work-around to this dumb behaviour is this:

1) Locate your Fallout.ini file.
2) Right click it and select Properties.
3) Disable Read Only and apply the change.
4) Open the INI file apply your desired changes. Save the changes.
5) Repeat Steps 1 & 2.
6) Select the Security tab.
7) Select Advanced.
8) Disable Inheritance. Select the top option when prompted and then Okay to close this Advanced window.
9) Edit each Group or Username and remove the Modify and Write permissions (only the "Read & Execute" and "Read" permissions are allowed). Apply the changes.

10) Play the game.

This will prevent the game from undoing your edits.

You could also use a mod manager like FOMM or Vortex. These managers have their own .ini files for the Fallout titles (along with script extenders pre-installed when the games are managed) that are loaded every time the game launches.