Some packages provided by texlive-latexextra have newer versions in the CTAN repository. If a user needs such a version but has texlive-latexextra installed, then there will be duplication of packages. There seem to be no conflict now since texlive installs in /usr/share/texmf-dist , while latex-package eclass installs in /usr/share/texmf. Still I think it will be "cleaner" to provide USE flags for all texlive-latexextra modules for selective installation. Reproducible: Always
If you are suggesting to add hundreds of USE flag for one ebuild, than that's not going to happen for sure, totally unmaintainable both for users and developers. If I misunderstood you and you have a more reasonable suggestion, then please clarify and reopen this bug.