To install some applications, we need to add a repository to the system. Why didn't the creators just put them into the Main or Universe repositories, though those applications have GPL license and they are not new (Grub Customizer for example). What is the cause of that?
main is supported by Canonical. Obviously they're not going to support every arbitrary piece of software on the internet. Software in
universe is inherited from Debian, where a select group of people, designated as Debian Developers, take responsibility for the maintenance of the packages they upload (even if the actual packaging is done by others). Obviously, they don't have the capability to maintain packages for every piece of software on the internet.
What do people do who can't get Canonical or Debian Developers to support their software? They must find other ways, which include creating their own repository. The introduction of the PPA by Ubuntu relieved a lot of pressure on community volunteers to maintain packages, and at the same time, freed developers from a lot of the constraints imposed by the release policies of distros.
Remember that what you want may not be what somebody else wants. By sticking to a stable set of software and allowing PPAs, while the users have a slight overhead of maintaining the list of repositories, they get a lot of flexibility in getting what they need. Developers get flexibility in providing updates. Maintainers are relieved of the pressure of having to keep up to date with every arbitrary piece of software on the internet.
In the particular case of GRUB Customizer, it is not packaged in Debian simply because no one has done the packaging work. There is a Request for Package bug opened for it, so anybody who is willing (and able) to do the packaging is welcome to do it. And it is not in Ubuntu because it is not in Debian.