Say, you have modified /etc/apache2/apache2-builtin-mods to have mod_alias.c compiled in statically: mod_alias static Then an "emerge apache" will result in apache without mod_alias.c - it won't neither be build statically nor as (dynamic) module. (No error nor warning appears to inform the user about this.) If you had a former installation of apache-2.0.58 in which this was not broken, this will result in malfunction of one's webserver.
This is only true if /etc/apache2 is not readably by user "portage".