I'm wondering, what are the disadvantages to using genkernel when I'm compiling a kernel in gentoo? Is it perfectly ok to use genkernel all in pretty much any situation, and skip this difficult/arduous part of the installation?
There are no disadvantages as far as I am aware of, other than the project lacking manpower; so, if you go for really specialized situations with the kernel, you might come across a bug or two.
Yes, you can use genkernel just fine for a lot of situations. You can find some basic configuration options in /etc/genkernel.conf if you need them.