Hi, welcome to the Sabayon Community
It is not true
that portage can easily lead to a damaged system.
It is true
that portage can easily lead to a damaged system if
you heavily mix it with entropy without
So, the best way to use Sabayon is to choose a main package manager, entropy or portage, whichever you like the most, and use it as your main manager, keeping the other one as an "emergency tool" or for the packages that are unavailable with the other one.
The USE flags can be easily viewed in the make.conf and package.use files, as you would do with Gentoo. If you want to customize your Sabayon installation, I suggest you to use a CoreCD version of Sabayon, then customize the make.conf and package.use files. After that, just rebuild everything with portage.
The flags are set or unset because those are the USE flags used to build the packages for entropy, since entropy is compatible with portage.
If you check the package.use
file, you will notice that many of the choices are documented.
Most of the times if you choose to change the flags, you will notice that many dependencies are pulled to perform the changes, or USE flags conflicts arise.
So the default USE flags are selected carefully to balance the dependencies, efficiency and usability of the system, in order to provide good entropy packages.