What you're saying is "maybe they should stop being Gentoo". The whole point of Gentoo is customization of your built-from-source packages. (As I recall, but it's been over a decade since I tried it so I might be remembering things wrong). Every optional feature in a piece of software, that would be controlled by some `--with-foo` option to `configure`, gets turned into a USE flag in Gentoo. Packages that have `--with-foo`, `--with-bar`, `--with-baz`, and `--with-quux` then have four USE flags, with 16 possible combinations of enabled or disabled. And the Gentoo maintainers team tries to make sure that all those combinations work, except for ones that obviously contradict each other.

So it's not Gentoo's decision to have so many flags, it's upstream's decision. I bet the Gentoo maintainers would love it if upstream acknowledged "okay, this 'optional' feature isn't really optional any longer". But they don't, and they continue to have dozens of flags, which Gentoo (due to their build philosophy) dutifully copied and tried to test — an overwhelming task.