package.conf.d should be under /var, not /usr
/usr is the second major section of the filesystem. /usr is shareable, read-only data. That means that /usr should be shareable between various FHS-compliant hosts and must not be written to. Any information that is host-specific or varies with time is stored elsewhere.
package.conf.d is not shareable, as different machines may have different packages installed, so we should put it under /var instead.