It's best to log in as root or su's to root when installing the packages. That way you are assured that all files are owned by user and group root (and not owned by the userid of the non-root user), and if a package wants to set special permissions, it can do so without problems due to non-root access.
The documentation that comes with Glibc, Gcc, and other packages recommend not to compile the packages as user root. We feel it's safe to ignore that recommendation and compile as user root anyway. Hundreds of people using LFS have done so without any problems whatsoever, and we haven't encountered any bugs in the compile processes that cause harm. So it's pretty safe (never can be 100% safe though, so it's up to you what you end up doing).