MariaDB /root/.my.cnf is always updated with the correct root password?

Only for initial install. If you change mysql root password yourself in future manually, then you need to manually update /root/.my.cnf as per MariaDB MySQL - CentminMod.com LEMP Nginx web stack for CentOS

Only time /root/.my.cnf is auto updated is if you use Centmin Mod 123.09beta01's centmin.sh menu option 11 submenu option 0 which allows resetting MySQL root user password when the known existing MySQL root password is contained in /root/.my.cnf as per MariaDB - How to reset MySQL root user password for CentOS 7 / MariaDB 10.1.19+

Code (Text):

--------------------------------------------------------
     Centmin Mod Menu 123.09beta01 centminmod.com     
--------------------------------------------------------
1).  Centmin Install
2).  Add Nginx vhost domain
3).  NSD setup domain name DNS
4).  Nginx Upgrade / Downgrade
5).  PHP Upgrade / Downgrade
6).  XCache Re-install
7).  APC Cache Re-install
8).  XCache Install
9).  APC Cache Install
10). Memcached Server Re-install
11). MariaDB MySQL Upgrade & Management
12). Zend OpCache Install/Re-install
13). Install/Reinstall Redis PHP Extension
14). SELinux disable
15). Install/Reinstall ImagicK PHP Extension
16). Change SSHD Port Number
17). Multi-thread compression: pigz,pbzip2,lbzip2...
18). Suhosin PHP Extension install
19). Install FFMPEG and FFMPEG PHP Extension
20). NSD Install/Re-Install
21). Update - Nginx + PHP-FPM + Siege
22). Add Wordpress Nginx vhost + Cache Plugin
23). Update Centmin Mod Code Base
24). Exit
--------------------------------------------------------
Enter option [ 1 - 24 ] 11
--------------------------------------------------------

Code (Text):

--------------------------------------------------------
     MariaDB MySQL Upgrade & Management Sub-Menu       
--------------------------------------------------------
0). Regenerate New MySQL Root User Password (local server)
1). MariaDB 5.2.x Branch Upgrade Only
2). MariaDB 5.2.x to MariaDB 5.5 YUM upgrade
3). MariaDB 5.5 to MariaDB 10.x YUM upgrade
4). MariaDB 5.5 to MariaDB 10.1.x YUM upgrade
5). MariaDB 10.x to MariaDB 10.1.x YUM upgrade
6). MariaDB 10.1.x to MariaDB 10.2.x YUM upgrade
7). Back to Main menu
--------------------------------------------------------
Enter option [ 0 - 7 ] 0
--------------------------------------------------------

This routine will reset the MySQL root user password
and properly update the /root/.my.cnf file as well.

This routine is only for local MariaDB MySQL servers not remote ones

Do you want to continue? [y/n]: