How to stop MySQL recreating SSL files on restart
From the documentation page you linked to:


  This variable is available if the server was compiled using OpenSSL 


It sounds like you're using the standard MySQL community edition binary distribution, which is not compiled with OpenSSL, and this is why you're getting the error message when you try to start up with auto_generate_certs=OFF.

See OpenSSL vs yaSSL for details. 

See also documentation for the ssl_capath variable, which is what I assume you looked at to deduce that MySQL was looking for your certificate files in /etc/mysql/ssl:


  MySQL distributions compiled using OpenSSL support the --ssl-capath option (see Section 6.4.4, “OpenSSL Versus yaSSL”). Distributions compiled using yaSSL do not because yaSSL does not look in any directory and does not follow a chained certificate tree. yaSSL requires that all components of the CA certificate tree be contained within a single CA certificate tree and that each certificate in the file has a unique SubjectName value. To work around this yaSSL limitation, concatenate the individual certificate files comprising the certificate tree into a new file and specify that file as the value of the --ssl-ca option.