When changing the config file to something I like in game and directly in the file everything goes well, but as soon as I startup the game, It changes the config file to default automatically and doesn't save the changes, is there anyway to resolve this?

Fixed in 1.12.2-0.2.8-pre6. Its a pretty unstable version but work on back porting 0.2.9 (the 1.13.2 code to 1.12.2) is very slow so its the best that I've got for 1.12.2.