My guess is that GUI tools often clobber configuration files once they touch them, because it's easier to write code that stores configuration as a hashmap and when it saves it back, the output is not going to preserve things like, user comments, the order of things, etc.

Is it really though? And why are we just calling out GUI tools? Command line tools also must read in a config file, and they manage with text. json, ini, yaml, xml parses and writers exist in every language. There really isn't an excuse to not use a text-based config.

If the Windows registry + INI files + config files anyway is the alternative, I'll take the text files please.

I think command line tools (like say, git-config) manage one option at a time.

GUI tools tend to manage everything at once. Imagine the giant options box from MS Word 2003.

It still has to read in the current config, mutate it, and write it out.

I guess they mean that because GUI tools often have, well, a GUI to change options, they tend to write their configuration files. Whereas for command-line tools it's rare that they provide methods for changing their options and thus they tend to only read their config, thus never running into the problem of clobbering user edits.

Mind you, there are plenty of GUI applications that get this right anyway. But usually for the vast majority of users there is never a need of mangling configuration files by other means.