So far, I can get it to work with a workaround: by re-initializing MySQL with the new value for lower_case_table_names after its installation. These are the requiered steps:

1. Install MySQL:
   

   sudo apt-get update    
   
   sudo apt-get install mysql-server -y
   
   

   
   


2. Stop the MySQL service:
   

   sudo service mysql stop
   
   

   
   


3. Delete the MySQL data directory:
   

   sudo rm -rf /var/lib/mysql
   
   

   
   


4. Recreate the MySQL data directory (yes, it is not sufficient to just delete its content):
   

   sudo mkdir /var/lib/mysql    
   
   sudo chown mysql:mysql /var/lib/mysql
   
   sudo chmod 700 /var/lib/mysql
   
   

   
   


5. Add lower_case_table_names = 1 to the [mysqld] section in /etc/mysql/mysql.conf.d/mysqld.cnf.


6. Re-initialize MySQL with --lower_case_table_names=1:
   

   sudo mysqld --defaults-file=/etc/mysql/my.cnf --initialize --lower_case_table_names=1 --user=mysql --console
   
   

   
   


7. Start the MySQL service:
   

   sudo service mysql start
   
   

   
   


8. Retrieve the new generated password for MySQL user root:
   

   sudo grep 'temporary password' /var/log/mysql/error.log
   
   

   
   


9. Change the password of MySQL user root either by:
   

   sudo mysql -u root -p
   
   

   
   and executing:
   

   ALTER USER 'root'@'localhost' IDENTIFIED BY 'MyNewPa$$w0rd';
   
   

   
   afterwards, OR by calling the "hardening" script anyway:
   

   sudo mysql_secure_installation
   
   

   
   

After that, you can verify the lower_case_table_names setting by entering the MySQL shell:

sudo mysql -u root -p

and executing:

SHOW VARIABLES LIKE 'lower_case_%';

Expected output:

+------------------------+-------+

| Variable_name          | Value |

+------------------------+-------+

| lower_case_file_system | OFF   |

| lower_case_table_names | 1     |

+------------------------+-------+