Per the discussion on -dev: http://archives.gentoo.org/gentoo-dev/msg_dc705dc2c1a45e18a85aa62e8fb17009.xml http://archives.gentoo.org/gentoo-dev/msg_829163256397bedb7c96e751347ee4d8.xml All packages that build kernel modules must offer USE=modules, which allows disabling the modules. The user may have built them directly as part of their kernel config (even if it was an external package, it can be patched into the kernel). All you do is NOT build or install the modules. The package still gets installed, even if it's going to be empty, so that the deptree is still preserved. Modules is being enabled in the base profile. So that they are built by default where the USE flag is introduced.
I'm going to close this, if this becomes an issue in the future, I think we can reopen with bugs as blockers to this tracker. Maybe this should be documented in the devmanual.