This is more a note to myself… but may also be useful with others who may be wondering WTF is wrong with their mod_auth_mysql setup.
To configure it, do it as per the instructions mentioned in the CONFIGURE file, or even following the /etc/apache2/modules.d/12_mod_auth_mysql.conf that the ebuild installs… HOWEVER… you will need to change the length of the password field in the MySQL code snippets to suit your encryption method.
I decided to use SHA1 hashes, which are 40 characters long (encoded as hex). Thus, you use a column type of CHAR(40), and set your authentication configuration to use AuthMySQLPwEncryption sha1. To use the “scrambled” encryption scheme (uses MySQL’s PASSWORD() function), this column needs to be 41 characters long, not the 20 advertised in the examples.
Once you do this, everything should be fine… and things will work as expected.