GUIs are way more complicated than you imagine, and require a completely different set of skills than developing the sort of program you mentioned.
If you want a nice, easy to use and well supported software, then pay for it and hold whoever you're paying accountable for making it user-friendly. If whatever you are using is free open source software, then that's literally !choosingbeggars
If you really think it's something that can be built in an afternoon, feel free to commission a freelancer to make the GUI for you or see if the repository owner is accepting any sort of bounties/commissions. How expensive could an afternoon's worth of work be?
Game engines have their own tools and languages, which can be very different from non-game software, and needless to say require a completely different skill set from your average software without a GUI.
Most of the time, they cannot easily interoperate with the languages people use for other things. When you are building a game, you will be using the engine's tools and language from the very start, but porting an existing software to work inside of a game engine is unrealistic, and building normal software inside of a game engine would be completely absurd for most cases, both for performance reasons and also for developer convenience.
In theory you might be able to pack the original program on its own with no changes and just make the GUI interact with the actual program, but at that point it's already a completely separate project from the original software - a project that the original developer likely has no interest in, assuming that the original program already fulfills their own needs.
In other words: While it is possible to use Godot and alike to create a GUI, for most cases you would have to either do some extremely complex things to run the original program inside of the engine or (re)write the entire program from scratch inside of the engine, and odds are the engine will not have direct equivalents of third-party tools the program relies on.