Sadly, there used to be a standard GUI config file called .Xdefaults, and even a tool called editres to edit it, but too many of the newer toolkits have ignored it and rolled their own.
As for cut and paste, once it was standard, then otehr people came in most notably trying to force Windows' conventions into Linux ignoring UNIX history. Maybe as with Xdefaults, people rolling their own instead of finding out what the system already used is the cause of inconsistancy. Fortunately, cut and paste is steadily being fixed.
The gripe I submitted concentrated mainly on such situations where a developer, sometimes a big corporate that should know better, has released applications for Linux that think they're on Windows. I've seen some applications try to show the Linux filesystems as Windows style drive letters!