When using genkernel as opposed to make && make modules_install, I find that scripts/genksyms/genksyms is missing as is Module.symvers. These files are still present when doing the manual method, but allow for userspace utilities such as alsa-drivers to be installed.
Correct... genkernel normally cleans up after itself. Call external ebuilds using the --callback functionality, such as --callback="emerge alsa-drivers" and you should have no issues.
Let's ask it frankly: after using genkernel, have you any trouble getting alsa-drivers work ? If no, then, there is no bug. If you are installing manually your drivers, I am not sure you can expect Gentoo's tools to be 100% compliant with that. Any problem with update-modules ? I d say there is a bug if it had prevent you from emerging anything. Does not seem to be the case. => I think it's INVALID bug.
I don't use genkernel anymore, and given the --callback functionality, I'm inclined to agree with you.