In asterisk.conf I have these directories set:
[directories](!)
astcachedir => /tmp
astetcdir => /etc/asterisk
astmoddir => /usr/lib64/asterisk/modules
astvarlibdir => /var/lib/asterisk
astdbdir => /var/spool/asterisk
astkeydir => /var/lib/asterisk     
astdatadir => /var/lib/asterisk
astagidir => /var/lib/asterisk/agi-bin
astspooldir => /var/spool/asterisk
astrundir => /run/asterisk
astlogdir => /var/log/asterisk
astsbindir => /usr/sbin

A number of these directories are ignored when installing Asterisk 18.12.1-1.el9.1 from EPEL, and cannot be changed. Output from "core show settings":
* Directories
  -------------
  Configuration file:          /etc/asterisk/asterisk.conf
  Configuration directory:     /etc/asterisk
  Module directory:            /usr/lib64/asterisk/modules
  Spool directory:             /var/spool/asterisk
  Log directory:               /var/log/asterisk
  Run/Sockets directory:       /run/asterisk
  PID file:                    /run/asterisk/asterisk.pid
  VarLib directory:            /usr/share/asterisk
  Data directory:              /usr/share/asterisk
  ASTDB:                       /var/spool/asterisk/astdb
  IAX2 Keys directory:         /usr/share/asterisk/keys
  AGI Scripts directory:       /usr/share/asterisk/agi-bin


I do not encounter this problem when running Asterisk 18.17.0, as installed from my own RPMs (which are built based on the EPEL spec files.)