package.conf.d should be under /var, not /usr
fhs-2.3 says:
/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.