When you choose to install an updated grsec kernel over your default gentoo kernel you might run into a few problems. I noticed "/usr/include/linux" this should be a symlinked to /usr/src/linux/include but is not. I had to change that in order to keep my system running smooth. As far as it breaking emerge it wont but you have to be carefull when your doing emerge world's, as that might try to install gentoo-sources, gentoo-kernel which could kill your symlinks. In addition you could email
aliz@gentoo.org and request that there team sync up versions to whats currently "stable" in grsec.
I think the gentoo grsec patch that comes with gentoo-sources-2.4.20 is grsec 19.7