The reason why mods are so incompatible if they edit the same file is because the system the game uses basically requires you to tell it what file to look at, and then give it a specific line number to add/remove code for. So if the line numbers are changed because one mod completely overwrites the file then it will change the wrong thing or insert the code in the wrong place and then it may work (if it doesn't necessarily matter where in a function the code is and doesn't accidentally drop it in the middle of some if or for) but it may also break everything.