It wouldn't be very hard to merge updates to the file in an automated fashion. You can use programs like
WinMerge to automatically see all of the differences between two versions of a file. All you have to do is compare the stock 1.20 file with the stock 1.25 file to see every single change, then copy the changes into your custom file. WinMerge is especially great for keeping your mod's Settings.txt file up to date.
But if all you are doing is reordering a component file based on certain criteria, a quick program/script could be written to do it automatically once the criteria are determined.