mod_auth_mysql (including version 3.0.0) does actually not work with Apache >=2.1. Thus please correct to: RDEPEND="<net-www/apache-2.2.0"
This is something we will fix before we unmask the 2.2 version of apache. I'm sure there are many other modules that also won't work with 2.2.
The last I heard, Apache 2.2.x uses a different API for modules (or something like that) - the developers of mod_auth_mysql were not even sure that they were going to do the neccessary modifications to make it compatible, as 2.2.x may have alternative authentication techniques available.
I just commited a revision bump including a patch from the UPSTREAM patch tracker. This should hopefully fix the issues with =apache-2.2*. Feel free to reopen if not.