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.