I am facing similar issue (using Tomcat Bitnami Google Click to Deploy). My server.xml is nearly similar as above, except that my keystoreFile, Pass, SSL File and SSL Key Files are located in $HOME instead of /opt/bitnami/....
In my case, Tomcat does start and work as expected, BUT an old certificate (issued to and by example.com) is getting picked up. Despite me having purchased and installed a new certificate.
Interestingly, in my Spring Boot web application, the "embedded" Tomcat does show the new certificate when run on localhost. But when I take my .war to Compute Engine Tomcat Bitnami, it's just picking up
CN = example.com
OU = Certificate generated at boot time
O = Bitnami
Can you please help.
I am assuming I need to configure Tomcat. Haven't changed Apache HTTPD files at /opt/bitnami/apache2/conf.